Prepared in Cooperation with the City of Palo Alto, California

Near-Field Receiving Water Monitoring of Trace Metals 

and a Benthic Community Near the Palo Alto Regional 

Water Quality Control Plant in South San Francisco Bay, 

California: 2015

Open File Report 2016–1118

U.S. Department of the Interior

U.S. Geological Survey
Cover Image:

Marsh and mudflat at Sand Point, Baylands Nature Preserve, Palo Alto, Calif. Photo courtesy of Dan Cain, USGS, 

2014. 
Prepared in cooperation with the City of Palo Alto, California 

Near-Field Receiving Water Monitoring of Trace Metals 

and a Benthic Community Near the Palo Alto Regional 

Water Quality Control Plant in South San Francisco Bay, 

California: 2015

By Daniel J. Cain, Janet K. Thompson, Jeff Crauder, Francis Parchaso, Robin Stewart, Mathew Turner, Michelle I. 

Hornberger, and Samuel N. Luoma

Open-File Report 2016–1118

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Director

U.S. Geological Survey, Reston, Virginia: 2016

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Suggested citation:

Cain, D.J., Thompson, J.K., Crauder, Jeff, Parchaso, Francis, Stewart, Robin, Turner, Mathew, Hornberger, M.I., 

and Luoma, S.N., 2016, Near-field receiving water monitoring of trace metals and a benthic community near the 

Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California; 2015: U.S. Geological 

Survey Open-File Report 2016–1118, 78 p., http://dx.doi.org/10.3133/ofr20161118.

ISSN 2331-1258 (online)
iii

Contents

Executive Summary of Past Findings ......................................................................................................................... 1

Abstract ...................................................................................................................................................................... 3

Introduction................................................................................................................................................................. 4

Methods...................................................................................................................................................................... 7

Sampling Frequency and Duration.......................................................................................................................... 7

Measurements of Metal Exposure........................................................................................................................... 7

Sediment ............................................................................................................................................................. 7

Clam Tissue ........................................................................................................................................................ 8

Sample Preparation and Analysis for Metals, Excluding Mercury and Selenium .................................................... 8

Sample Preparation and Analysis for Mercury and Selenium ................................................................................. 8

Quality Assurance................................................................................................................................................... 9

Salinity .................................................................................................................................................................... 9

Other Data Sources .............................................................................................................................................. 10

Biological Response.............................................................................................................................................. 10

Condition Index ................................................................................................................................................. 10

Reproductive Activity......................................................................................................................................... 10

Community Analysis.......................................................................................................................................... 10

Results...................................................................................................................................................................... 11

Salinity .................................................................................................................................................................. 11

Sediments ............................................................................................................................................................. 11

Clam Tissue ...................................................................................................................................................... 12

Reproduction of Macoma petalum..................................................................................................................... 13

Benthic Community ........................................................................................................................................... 14

Summary .................................................................................................................................................................. 17

Long-Term Observations ...................................................................................................................................... 17

2015 Observations................................................................................................................................................ 19

Value of Long-Term Monitoring............................................................................................................................. 20

Selected References ................................................................................................................................................ 20

Appendix 1. Certified concentrations and the percent recoveries of inorganic elements in National Institute of 

Science and Technology Standard Reference Material 2709a (San Joaquin Soil) and 2711a (Montana Soil) 

prepared in 2015....................................................................................................................................................... 67

Appendix 2. Certified concentrations and the percent recoveries of inorganic elements in National Institute of 

Science and Technology Standard Reference Material 2976 (Mussel Tissue) and 1566b (Oyster Tissue) prepared 

in 2015...................................................................................................................................................................... 68

Appendix 3. Mercury and selenium concentrations determined in sample splits of surface sediments and Macoma 

petalum collected at Palo Alto, Calif., 2015............................................................................................................... 69

Appendix 4. Certified and measured concentrations of mercury and selenium in standard reference materials 

analyzed in 2015....................................................................................................................................................... 69

Appendix 5. Method detection limits and reporting levels for inductively coupled plasma-optical emission 

spectrophotometry methods. .................................................................................................................................... 70

Appendix 6. Statistical summary of percentage of sediment in samples composed of clay- and silt-sized particles, 

collected from Palo Alto, Calif., 1994–2015. ............................................................................................................. 71

Appendix 7. Statistical summary of silver and copper concentrations in sediment and the clam Macoma petalum, 

Palo Alto, Calif., for 2015 and 1977–2015. ............................................................................................................... 72
iv

Appendix 8. Complete list of benthic species found at Palo Alto in the year 2015................................................... 73

Appendix 9. Benthic species name changes as of 2015.......................................................................................... 77

Figures

 1. Location of the Palo Alto sampling site in South San Francisco Bay, Calif......................................... 25

 2. Precipitation recorded at San Francisco WB AP in San Mateo County, CA. ...................................... 26

 3. Surface-water salinity in parts per thousand (ppt) at the Palo Alto site, Calif., 1994–2015. Top panel 

 illustrates seasonal variation as the monthly averages (±1 std, n = 21). The bottom panel shows

 individual monthly data (dots) and the running average (solid line) indicating the long-term pattern 27

 4. Aluminum, iron, and silt/clay in sediments, Palo Alto, Calif., 1994–2015............................................ 28

 5. Chromium and nickel in sediments, Palo Alto, Calif., 1994–2015....................................................... 29

 6. Copper in sediments, Palo Alto, Calif., 1994–2015 ............................................................................ 30

 7. Zinc in sediments, Palo Alto, Calif., 1994–2015 ................................................................................. 31

 8. Silver in sediments, Palo Alto, Calif., 1994–2015 ............................................................................... 32

 9. Mercury and selenium in sediments, Palo Alto, Calif., 1994–2015 ..................................................... 33

 10. Annual mean copper concentrations in the clam Macoma petalum, Palo Alto, Calif., 1977–2015 ..... 34

 11. Annual mean silver concentrations in the clam Macoma petalum, Palo Alto, Calif., 1977–2015........ 35

 12. Copper concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015........................... 36

 13. Silver concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015 ............................. 37

 14. Chromium concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015...................... 38

 15. Nickel concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015............................. 39

 16. Zinc concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015................................ 40

 17. Mercury concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015 ......................... 41

 18. Selenium concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015 ....................... 42

 19. Condition index of the clam Macoma petalum, Palo Alto, Calif., 1988–2015...................................... 43

 20. Reproductive activity of the clam Macoma petalum, Palo Alto, Calif., 1974–2015 ............................. 44

 21. Reproductive activity of the clam Macoma petalum, Palo Alto, Calif., 2011–2015 ............................. 45

 22. Total number of species present at the Palo Alto site, Calif., 1974–2015........................................... 46

 23. Total average number of individuals present at the Palo Alto site, Calif., 1974–2015 ........................ 47

 24. Monthly average abundance of Macoma petalum, Palo Alto, Calif., 1974–2015................................ 48

 25. Monthly average abundance of Mya arenaria, Palo Alto, Calif., 1974–2015 ...................................... 49

 26. Monthly average abundance of Gemma gemma, Palo Alto, Calif., 1974–2015.................................. 50

 27. Monthly average abundance of Ampelisca abdita, Palo Alto, Calif., 1974–2015................................ 51

 28. Monthly average abundance of Streblospio benedicti, Palo Alto, Calif., 1974–2015 .......................... 52

 29. Monthly average abundance of Grandiderella japonica, Palo Alto, Calif., 1974–2015 ....................... 53

 30. Monthly average abundance of Neanthes succinea, Palo Alto, Calif., 1974–2015............................. 54

 31. Monthly average abundance of Heteromastus filiformis, Palo Alto, Calif., 1974–2015....................... 55

 32. Monthly average abundance of Nippoleucon hinumensis, Palo Alto, Calif., 1974–2015 .................... 56

 33. Reproductive mode annual abundance with silver concentrations in the clam Macoma petalum and 

 in sediment, Palo Alto, Calif., 1974–2015 ........................................................................................ 57

34. Reproductive mode annual abundance with copper concentrations in the clam Macoma petalum

 and in sediment, Palo Alto, Calif., 1974–2015 ................................................................................. 58

 35. Feeding mode annual abundance with silver concentrations in the clam Macoma petalum and in

 sediment, Palo Alto, Calif., 1974–2015 ............................................................................................ 59
v

36. Feeding mode annual abundance with copper concentrations in the clam Macoma petalum and in

 sediment, Palo Alto, Calif., 1974–2015 ............................................................................................ 60

37. Species rank-abundance for the benthic community, Palo Alto, Calif., for 1977, 1989, 2002, and 

 2015................................................................................................................................................. 61

38. Species rank-abundance identified by feeding mode, Palo Alto, Calif., for 1977, 1989, 2002, and 

 2015................................................................................................................................................. 62

39. Species rank-abundance data identified by reproductive mode, Palo Alto, Calif., for 1977, 1989, 

 2002, and 2015................................................................................................................................ 63

Tables

 1. Concentrations of major and minor inorganic elements, total organic carbon, percent of fine particles 

 in surface sediments, and salinity of water pooled on the surface of sediments for samples

 collected from Palo Alto, Calif., 2015 ................................................................................................ 64

 2. Concentrations of trace metals in and the condition index for the clam Macoma petalum, Palo Alto, 

 Calif., 2015........................................................................................................................................ 65

 3. Reproduction data for Macoma petalum, Palo Alto, Calif., 2015 .......................................................... 66
vi

Conversion Factors

Multiply By To obtain

foot (ft) 0.3048 meter (m)

gallon (gal) 3.785 liter (L)

inch (in) 2.54 centimeter (cm)

inch (in) 25,400 micrometer (μm)

meter (m) 1,000,000 micrometer (μm)

mile (mi) 1.609 kilometer (km)

ounce (oz) 28.35 gram (g)

part per million (ppm) 1 microgram per gram (μg/g)

milligram per kilogram (mg/kg) 1 microgram per gram (μg/g)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows:

°C=(°F-32)/1.8

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) or micrograms per liter (μg/L).

NOTE TO USGS USERS: Use of liter (L) as a special name for cubic decimeter (dm3) is restricted to the measurement of liquids and 

gases. No prefix other than milli should be used with liter.
vii

Abbreviations and Acronyms

mL milliliter

μΏ-cm microohm per cm

μg/g microgram per gram

mg/kg milligram per kilogram

μm micrometer

CI condition index

ERL effects range-low 

ERM effects range-median

ICP-OES inductively coupled plasma-optical emission spectrophotometry

IRMS isotopic ratio mass spectrophotometry

MDL method detection limit

MLLW mean low low water

MRL method reporting level

NIST National Institute of Standards and Technology

NPDES National Pollutant Discharge Elimination System 

PARWQCP Palo Alto Regional Water Quality Control Plant 

RWQCB California Regional Water Quality Control Board

SFEI San Francisco Estuary Institute 

USEPA U.S. Environmental Protection Agency

USGS U.S. Geological Survey
Near-Field Receiving Water Monitoring of Trace Metals 

and a Benthic Community near the Palo Alto Regional 

Water Quality Control Plant in South San Francisco Bay, 

California: 2015

By Daniel J. Cain, Janet K. Thompson, Jeff Crauder, Francis Parchaso, Robin Stewart, Mathew Turner, Michelle I. 

Hornberger, and Samuel N. Luoma 

Executive Summary of Past Findings

U.S. Geological Survey (USGS) personnel have assessed trace-metal concentrations in 

sediments and sediment-dwelling species since 1977 at an intertidal site in the vicinity of the discharge 

of the Palo Alto Regional Water Quality Control Plant (PARWQCP). They have also profiled that area's 

benthic community structure since 1974. Ancillary biotic and abiotic factors that could affect metal 

concentrations and benthic community structure—exotic species invasions, pelagic food availability, 

and weather anomalies—have also been measured during this time. Collectively, this dataset describes a

long-term, detailed history of metal concentrations and benthic community dynamics at this site. 

Initially, these studies found exceptionally high concentrations of copper (Cu) and silver (Ag) in 

mud-dwelling animals in this area, with strong seasonal variability. Additional studies identified the 

PARWQCP as a point source for Cu and Ag and established the clam Macoma petalum as a biological 

indicator of metal exposure. The annual mean concentrations of Cu and Ag in Macoma petalum were 

287 milligrams per kilogram (mg/kg) and 105 mg/kg, respectively, in 1980. These levels exceeded 

tissue concentrations reported in the literature for this species and were much greater than seen 

elsewhere in San Francisco Bay. Elevated metal concentrations coincided with reduced reproductive 

activity in M. petalum. Related studies supported the theory that elevated Ag concentrations inhibited 

the development of reproductive tissue. The benthic community also showed signs of environmental 

stress during this time. Opportunistic organisms that are capable of fast invasion and propagation in 

disturbed environments, such as the amphipod Ampelisca abdita, dominated the community. These 

organisms thrived on the surface of the mud in tubes or as shelled animals, brooded their young, and fed 

on waterborne particles.

Concentrations of Cu and Ag in both sediments and clams declined significantly during the 

1980s as the PARWQCP implemented more advanced wastewater treatment and source control 

programs. The downward trends in Cu in sediments and in the tissues of M. petalum correlated with 

reduced Cu discharge from the PARWQCP. Coincident with the decline in Cu and Ag in the sediment 

and clams, the reproductive activity of the clam greatly increased. The composition of the benthic 

community also shifted during this period. Opportunistic species became less dominant, and other 

species became more persistent. Other environmental factors that vary seasonally and annually (for 

example, sediment composition, grain-size distribution, organic content, and ambient water salinity)

were not associated with the observed temporal trends in metal concentrations, inferred metal effects on 

species, and benthic community changes. The only unidirectional change in an environmental factor 
2

during this period (1980–1990) was the decline in metal concentrations in discharge from the waste 

treatment plant.

Following the significant reductions in the 1980s, concentrations of Cu and Ag in sediments and 

clams have remained relatively low and stable. Concentrations have fluctuated modestly and without a 

sustained temporal trend. However, Ag in sediments remains greater than what may be considered the 

regional background (0.09 mg/kg). This persistent, low level of contamination likely derives from Ag 

introduced to the site before the 1990s. The concentrations of Cu and Ag in M. petalum have fluctuated 

as much as four-fold. Concentration minima for Cu observed during this period (1991, 2000–2005, and 

2008–2012) were comparable to what can be considered baseline concentrations for this species in San 

Francisco Bay (20–30 mg/kg). Thus, metal concentrations in sediments and tissue of M. petalum are 

more likely a combination of inputs from the PARWQP and other regional sources, cycling of 

contaminants stored within sediments, and regionally-scaled physical and biogeochemical processes 

controlling the distribution and bioavailability of metals.

As concentrations of Ag and Cu in M. petalum declined, reproductive activity increased both in 

terms of the percentage of individuals that were in a reproductively active stage and the frequency of 

reproductive activity during the year. Overall, the reproductive status of the population has improved 

and stabilized over the 20 years of reduced exposure to Ag and Cu at the site. 

Over the same period, the composition of the infaunal community shifted from a dominance of 

surface-dwelling, brooding species to species with various life-history characteristics. In particular, 

species that lay their eggs in the mud and feed by burrowing through and consuming the mud, which 

were rare in the community in the 1970s and 1980s, have increased in abundance. This pattern 

continued through 2007, with the less opportunistic species becoming more dominant in abundance. A 

disturbance occurred on the mudflat in early 2008 (possible causes include sediment accretion or 

freshwater inundation) that resulted in the loss of the benthic animals, except for those deep-dwelling 

animals like M. petalum. Animals returned to the mudflat within 2 months of the event, however, which 

suggested that the disturbance was not due to a persistent toxin or to anoxia. Benthic community data in 

2009 showed that the animals that returned to the mudflat were those that can respond successfully to a 

physical, nontoxic disturbance. The most recent community surveys showed a mix of animals that 

consume the sediment, filter feed, brood their young, and have pelagic larvae that must survive life on

the sediment at a young age. The 2008 defaunation event allowed for an examination of the response of 

the community to a natural disturbance and a comparison of this recovery to the long-term recovery 

observed in the 1970s, when the decline in sediment pollutants was the dominating factor. Today, the 

community at this site is very similar to the benthic community observed by Thompson and Parchaso 

(2012) throughout South San Francisco Bay: although small filter feeding species are numerically 

dominant, there is a significant proportion of the community that feeds on surface and subsurface 

sediment particles, a feature of community structure that is not present where sediments have high 

concentrations of toxicants. 

When this study started in the late 1970s, the site was already heavily contaminated with metals. 

Although the authors assume that the biological conditions reflected the consequences of elevated metal 

exposures, there is a scarcity of preexisting data to evaluate impacts due to elevated metals. However, 

the long-term record contained in this study provides a unique opportunity to document biological 

response when the stress of metal exposure is relaxed. The data make a compelling case that the 

mitigation of Ag and Cu in wastewater effluent during the 1980s allowed for biological recovery and the 

establishment of a more diverse and stable infaunal community. 
3

Abstract

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as 

Macoma balthica), clam reproductive activity, and benthic macroinvertebrate community structure were 

investigated in a mudflat 1 kilometer south of the discharge of the Palo Alto Regional Water Quality 

Control Plant (PARWQCP) in South San Francisco Bay, California. This report includes data collected 

by U.S. Geological Survey (USGS) scientists for the period from January 2015 to December 2015. 

These data are appended to long-term datasets extending back to 1974, and serve as the basis for the 

City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. 

Following significant reductions in the late 1980s, silver (Ag) and copper (Cu) concentrations in 

sediment and M. petalum appear to have stabilized. Data for other metals, including chromium (Cr), 

mercury (Hg), nickel (Ni), selenium (Se), and zinc (Zn), have been collected since 1994. Over this 

period, concentrations of these elements have remained relatively constant, aside from seasonal 

variation that is common to all elements. In 2015, concentrations of Ag and Cu in M. petalum varied 

seasonally in response to a combination of site-specific metal exposures and annual growth and 

reproduction, as reported previously. Seasonal patterns for other elements, including Cr, Ni, Zn, Hg, and 

Se, were generally similar in timing and magnitude as those for Ag and Cu. In M. petalum, all observed 

elements showed annual maxima in January–February and minima in April, except for Zn, which was 

lowest in December. In sediments, annual maxima also occurred in January–February, and minima were 

measured in June and September. In 2015, metal concentrations in both sediments and clam tissue were 

among the lowest on record. This record suggests that regional-scale factors now largely control 

sedimentary and bioavailable concentrations of Ag and Cu, as well as other elements of regulatory 

interest, at the Palo Alto site. 

Analyses of the benthic community structure at the same mudflat over a 40-year period show 

that changes in the community have occurred concurrent with reduced concentrations of metals in the 

sediment and in the tissues of the biosentinel clam, M. petalum, from the same area. Analysis of M. 

petalum shows increases in reproductive activity concurrent with the decline in metal concentrations in 

the tissues of this organism. Reproductive activity is presently stable (2015), with almost all animals 

initiating reproduction in the fall and spawning the following spring. The entire infaunal community has 

shifted from being dominated by several opportunistic species to a community where the species are 

more similar in abundance, a pattern that indicates a more stable community that is subjected to fewer 

stressors. In addition, two of the opportunistic species (Ampelisca abdita and Streblospio benedicti) that 

brood their young and live on the surface of the sediment in tubes have shown a continual decline in 

dominance coincident with the decline in metals; both species had short-lived rebounds in abundance in 

2008, 2009, and 2010 and showed signs of increasing abundance in 2015. Heteromastus filiformis (a 

subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles 

residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed an increase in 

dominance, concurrent with the decrease in Ag and Cu concentrations, and in the last several years 

before 2008, showed a stable population. H. filiformis abundance increased slightly in 2011–2012 and 

returned to pre-2011 abundance in 2015. An unidentified disturbance occurred on the mudflat in early 

2008 that resulted in the loss of the benthic animals, except for deep-dwelling animals like M. petalum. 

However, within two months of this event animals returned to the mudflat. The resilience of the 

community suggested that the disturbance was not due to a persistent toxin or to anoxia. The 

reproductive mode of most species present in 2015 is reflective of species that were available either as 

pelagic larvae or as mobile adults. Although oviparous (live-birth) species were lower in number in this 

group, the authors hypothesize that these species will return slowly as more species move back into the 

area. The use of functional ecology was highlighted in the 2015 benthic community data, which showed
4

that the animals that have now returned to the mudflat are those that can respond successfully to a 

physical, nontoxic disturbance. Today, community data show a mix of species that consume the 

sediment, or filter feed, have pelagic larvae that must survive landing on the sediment, and those that 

brood their young. USGS scientists view the 2008 disturbance event as a response by the infaunal 

community to an episodic natural stressor (possibly sediment accretion or a pulse of freshwater), in 

contrast to the long-term recovery from metal contamination. We will compare this recovery to the 

long-term recovery observed after the 1970s when the decline in sediment pollutants was the 

dominating factor. 

Introduction

Determining spatial distributions and temporal trends in trace metals in sediments and benthic 

organisms is common practice for monitoring environmental contamination. These data can be the basis 

for assessing metal exposure and the potential for adverse biological effects. Another common method 

of environmental monitoring is to examine the community structure of sediment-dwelling benthic 

organisms (Simon, 2002). Spatial and temporal changes in community structure reflect the integrated 

response of resident species to environmental conditions, although the underlying cause(s) for the 

response may be difficult to identify and quantify. Together, measurements of metal exposure and 

biological response can provide a more complete view of anthropogenic disturbances and the associated 

effects on ecosystem health.

Sediment particles can strongly bind metals, effectively removing them from solution. As a 

result, sediments may accumulate and retain metals released to the environment. Contaminated 

sediments may become a chronic source of metals to the environment. Thus, concentrations of metals in 

sediments serve as a record of metal contamination in an estuary, with some integration over time. 

Fluctuations in the record may be indicative of changes in anthropogenic releases of metals into the 

environment (Förstner and Wittmann, 1979). 

Metals in sediments are also indicative of the level of exposure of benthic animals to metals 

through contact with, and ingestion of, bottom sediments and suspended particulate materials. However, 

geochemical conditions of the sediment affect the biological availability of the bound metals. 

Assimilation of bioavailable sediment-bound metal by digestive processes and the contribution of this 

source of metals relative to metals in the aqueous phase are not well understood. Thus, in order to better 

estimate bioavailable metal exposures, the tissues of the organisms themselves may be analyzed for 

trace metals. Benthic organisms concentrate most metals to levels higher than those that occur in 

solution (Phillips and Rainbow, 1993). Therefore, the record of metal concentrations in clam tissue can 

be a more sensitive indicator of anthropogenic metal inputs than the sediment record. Different species 

concentrate metals to different degrees. However, if one species is analyzed consistently, the results can 

be used to indicate trace-element exposures to the local food web. 

Contaminants can adversely affect benthic organisms at several organizational levels. For 

example, responses to a pollutant at the cellular or physiological level of an individual can result in 

changes at the population level, such as reductions in growth, survival, and reproductive success 

(Newman, 1998). Community level responses to population level impairment can include overall shifts 

in species abundance, favoring metal-tolerant species, which can result in changes in predator/prey 

interactions and competition for available resources. Changes in the benthic community can ultimately 

result in changes at the ecosystem level due to that community’s importance as primary consumers in 

the cycling of carbon in aquatic environments (Alpine and Cloern [1992] provides a local example).

In all aquatic environments, benthic organisms may be exposed to contaminants at all life stages 

through a variety of routes—sediment, water, and food (Wang and Fisher [1999] provides a summary of 
5

the potential transport of trace elements through food). Toxicant exposure is related to contaminant 

concentration as well as duration. Even at relatively low contaminant levels, long-term exposure can 

affect benthic organisms (Long and others, 1995). The added complexity of synergistic or antagonistic 

effects between different contaminants, and between contaminants and natural stressors, makes causal 

relationships difficult to identify and quantify, even on a site-specific basis. However, a time-integrated 

picture of ecosystem response to contaminant loading can be provided by field studies that link changes 

in exposure at multiple time scales (in this case seasonal to decadal) to changes at individual, 

population, and community levels. 

The California Regional Water Quality Control Board (RWQCB) has prescribed a selfmonitoring program with its reissuance of the National Pollutant Discharge Elimination System 

(NPDES) permits for South San Francisco Bay dischargers. The recommendation includes specific 

receiving-water monitoring requirements. 

Since 1994, the Palo Alto Regional Water Quality Control Plant (PARWQCP) (fig. 1) has been 

required to monitor metals and other specified parameters in sediments and the clam Macoma petalum

at an inshore location in South San Francisco Bay, Calif. In addition to the required monitoring, 

PARWQCP has undertaken monitoring of the benthic community as a whole. The monitoring protocols 

have been designed to be compatible with or complementary to the RWQCB’s Regional Monitoring 

Program. In this report, the USGS monitoring study is described, and data collected during 2015 are 

presented within the context of more than 35 years of previous data collections and investigations by the 

USGS at this inshore location. 

The data collected during this study include trace-metal concentrations in sediments and clams, 

clam reproductive activity, and benthic community structure. These data and those reported earlier (for 

example, Hornberger and others, 2000a; Luoma and others, 1991, 1995a, 1996; Moon and others, 2005; 

Shouse and others, 2003, 2004; Thompson and others, 2002; Cain and others, 2006; Dyke and others, 

2011; 2012, 2014) were used to meet the following objectives:

 Provide data to assess seasonal and annual trends in trace-element concentrations in sediments and 

clams, reproductive activity of clams, and benthic community structure at a site designated in the 

RWQCB’s self-monitoring program guidelines for PARWQCP.

 Present the data within the context of historical changes in South San Francisco Bay and within the 

context of other locations in the Bay published in the international literature. 

 Coordinate inshore receiving water monitoring program for PARWQCP and provide data 

compatible with relevant aspects of the regional monitoring program. The near-field data will 

augment the regional monitoring program as suggested by the RWQCB.

 Provide data that could support other South San Francisco Bay issues or programs, such as 

development of sediment quality standards. 

Despite the complexities inherent in monitoring natural systems, the adopted approach has been 

effective in relating changes in near-field contamination to changes in reproductive activity of a clam 

(Hornberger and others, 2000b) and in benthic community structure (Kennish, 1998). This study, with 

its basis in historical data, provides a context within which future environmental changes can be 

assessed.

Metal concentrations were monitored in sediments and a resident clam species, Macoma 

petalum. Analysis of trace-metal concentrations in the sediments over time provides a record of metal 

contamination of the site. The concentration and bioavailability of sediment-bound metals are affected 

by hydrology and geochemical factors (Thomson-Becker and Luoma, 1985; Luoma and others, 1995b).

Thus, ancillary data, including grain-size distribution, organic carbon, aluminum and iron content of the 

sediment, regional rainfall, and surface salinity were collected to interpret seasonal, annual, and inter-
6

annual variation in metal concentrations. The tissue of M. petalum provides a direct measure of 

exposure to bioavailable metals. 

Biological response of the benthic community to metal exposure was examined at three levels of 

organization: individual, population, and community. At the individual level, concentrations of metals 

in the tissues of M. petalum were compared with physiological indicators. Two common animal 

responses to environmental stress are reduced growth and reproductive activity. Growth and 

reproduction in M. petalum occur on fairly regular seasonal cycles. Seasonally, a clam of a given shell 

length will increase somatic tissue weight as it grows during the late winter and spring (Cain and 

Luoma, 1990). Reproductive tissue increases during the early stages of reproduction and declines during 

and after spawning. These cycles can be followed with the condition index (CI), which is an indicator of 

the physiological condition of the animal. The CI is the total soft-tissue weight of a clam standardized to 

shell length (Cain and Luoma, 1990). Inter-annual differences in growth and reproduction, expressed in 

the CI, are affected by the availability and quality of food, as well as other stressors, such as pollutant 

exposure and salinity extremes. An earlier study (Hornberger and others, 2000b) has shown that 

reproductive activity of M. petalum has increased with declining metal concentrations in animals from 

this location. Therefore, CI and reproductive activity of M. petalum appear to be useful indicators of 

physiological stress by pollutants at this location and continue to be monitored in this study. 

At the population level, trends of the dominant benthic species were examined to see if certain 

species have been more affected than others by environmental change. It has been shown that most 

taxonomic groups have species that are sensitive to elevated Ag (Luoma and others, 1995b) and that 

some crustacean and polychaete species are particularly sensitive to elevated sedimentary Cu (Morrisey 

and others, 1996; Rygg, 1985). In addition, the benthic community was examined for changes in 

structure: that is, shifts in the species composition of the macroinvertebrate community resulting in a 

change in the function of the community. The authors hypothesized that a shift in community 

composition and potentially in the function of the benthic community in the ecosystem would result 

from changes in the concentrations of either specific metals or a combination of contaminants for 

several reasons. First, prior studies have shown that South San Francisco Bay benthic communities were 

dominated by opportunistic species in the 1980s (Nichols and Thompson, 1985a). These opportunistic 

species might become less dominant as environmental stressors decrease. Second, environmental 

pollutants may differentially affect benthic species that use different feeding and reproductive modes. 

An intertidal mudflat community, such as this study site, should include a combination of species that 

feed on particles in the water column, on settled and buried food particles in the mud, and on other 

organisms. The absence of any one of these feeding groups may show limitations on species as a result 

of environmental stressors that target specific feeding groups. For example, pollutants attached to 

sediment particles are likely to affect species that consume the sediment as part of their feeding mode

and (or) those species that lay their eggs in the sediment (Newman and Jagoe, 1996). 

Previous analysis of this community has shown no correlation between changes in the 

community and measured environmental parameters (salinity, air and water temperature, delta outflow, 

precipitation, chlorophyll a, sediment total organic carbon, and biological oxygen demand; Shouse, 

2002). The community data are compared only to trace-metal data in this report. 

The Palo Alto site (PA) includes the benthic community sampling site and the M. petalum and 

sediment sampling site, both adjacent to Sand Point in Palo Alto Baylands Nature Preserve on a mudflat 

on the western shore of San Francisco Bay (fig. 1). The site is 1 kilometer southeast of the intertidal 

discharge point of the PARWQCP. The sampling locations are approximately 12 meters (m) from the 

edge of the marsh and 110 centimeters (cm) above mean low low water (MLLW). 
7

The sediment and biological samples from this location reflect a response of the receiving waters 

to the effluent just beyond the location of discharge. Earlier studies (Thomson and others, 1984) have 

shown that dyes, natural organic materials in San Francisquito Creek, and waters in the PARWQCP 

discharge move predominantly south toward Sand Point, thereby affecting the mudflats in the vicinity of 

Sand Point. Thomson and others (1984) showed that San Francisquito Creek and the Palo Alto Yacht 

Harbor were minor sources of most trace elements compared to the PARWQCP. Based on spatial and 

temporal trends of Cu, Ag, and Zn in clams and sediments, the PARWQCP appeared to be the primary 

source of elevated metal concentrations at the PA site in the spring of 1980 (Thomson and others, 1984; 

Cain and Luoma, 1990). Metal concentrations in sediments and clams (M. petalum), especially Cu and 

Ag, have declined substantially since the original studies as more efficient treatment processes and 

source controls were employed (Hornberger and others, 2000b). Frequent sampling each year was 

necessary to characterize those trends because there was significant seasonal variability (Cain and 

Luoma, 1990; Luoma and others, 1985). This report characterizes data for the year 2015, thereby 

extending the long-term record at this site. 

Methods

Sampling Frequency and Duration

In dynamic ecosystems such as San Francisco Bay, the environmental effects of anthropogenic 

stressors are difficult to distinguish from natural seasonal changes. Sustained sampling at frequent 

intervals can characterize seasonal patterns, capture episodic events, and identify longer-term trends, 

thereby increasing the probability that anthropogenic effects can be identified. Analyses of early 

community data (1974–1983; Nichols and Thompson, 1985a,b) showed that benthic samples need to be 

collected at monthly to bimonthly intervals to distinguish between natural and anthropogenic effects. 

Therefore, data reported herein are based on samples collected on a bimonthly basis from the exposed 

mudflat at low tide between January and December. Samples collected in the field include surface 

sediment, the deposit-feeding clam M. petalum, surface water, and sediment cores for community 

analysis. Surface water, surface sediment, and M. petalum were not collected during the months of July, 

August, and November. Cores for benthic community analyses were not collected during the months 

May and July. Data on sediments, M. petalum, and surface water have been collected continuously since 

1977, while community data were collected during 1974–1990 and 1998 to the present (2015). 

Measurements of Metal Exposure

Metal concentrations in surficial sediments and in the soft tissues of M. petalum were interpreted 

as indicative of metal exposure to the broader benthic community. The collection and preparation of 

sediment and M. petalum samples have previously been described in detail (see, for example, Dyke and 

others, 2014). The following is an overview of those procedures. 

Sediment

Sediment samples were scraped from the visibly oxidized (brownish) surface layer (top 1–2 cm) 

of mud and later that day sieved through a 100-micrometer (μm) mesh polyethylene screen with 

distilled water to remove large grains that might bias interpretation of concentrations. The mesh size 

was chosen to match the largest grains typically found in the digestive tract of M. petalum. All chemical 

data reported herein were determined from the fraction that passed through the sieve (<100 μm), termed 

the “silt/clay fraction.” 
8

The percent silt/clay fraction of sediment samples was determined to provide some 

comparability with bulk sediment determinations such as that employed in the Regional Monitoring 

Program (San Francisco Estuary Institute, 1997). The sediment that did not pass through the sieve (>100 

μm)—termed the sand fraction—was collected, as was the silt/clay fraction (<100 μm) (see above). 

Each fraction was dried to constant weight, and their percent contributions to the bulk sample were 

determined gravimetrically.

The silt/clay fraction was subsampled to provide replicates weighing 0.4–0.6 grams (g). These 

were redried (70 oC), reweighed, and then digested by hot acid reflux (10 milliliters [mL] of 16 normal 

[N] nitric acid). This method provides a “near-total” extraction of metals from the sediment and is 

comparable to the recommended procedures of the U.S. Environmental Protection Agency (USEPA) 

and to the procedures employed in the regional monitoring program. Another set of replicate 

subsamples from the silt/clay fraction were directly extracted with 12 mL of 0.6 N hydrochloric acid 

(HCl) for 2 hours at room temperature. This partial extraction method extracts metals bound to sediment 

surfaces and is operationally designed to obtain a crude chemical estimate of bioavailable metal. 

Total organic carbon (TOC) concentrations were determined using a continuous flow isotope 

ratio mass spectrophotometer (IRMS) (table 1). Before the analysis, sediment samples were acidified 

with 12 N HCl vapor to remove inorganic carbon (Harris and others, 2001). 

Clam Tissue

Specimens of M. petalum were collected by hand on each sampling occasion. Typically, 60–120 

individuals were collected, representing a range of sizes (shell length). 

In the laboratory, the clams were removed from the containers and gently rinsed with deionized 

water to remove sediment. Clams were immersed in seawater diluted with deionized water as necessary 

to the equivalent of ambient salinity, and moved to a constant temperature room (12 oC) for 48 hours to 

allow for the egestion of sediment and undigested material from their digestive tracts. 

Sample Preparation and Analysis for Metals, Excluding Mercury and Selenium

The shell length of each clam was measured with electronic calipers and recorded digitally. 

Clams were separated into 1- or 2-millimeter (mm) size classes (for example, 10.00–10.99 mm or 

10.00–11.99 mm). The soft tissues from all of the individuals within a given size class were dissected 

from the shell and collected in preweighed 20-mL screw-top borosilicate glass vials to form a single 

composite sample for elemental analysis. The vials were transferred to a convection oven (70 oC). After 

the tissues were dried to constant weight, they were digested by reflux in subboiling 16 N nitric acid. 

The tissue digests were then dried and metals resolubilzed in 0.6 N hydrochloric acid for trace-metal

analysis. 

Sediment and tissue concentrations of aluminum (Al), chromium (Cr), copper (Cu), iron (Fe), 

nickel (Ni), silver (Ag), and zinc (Zn) were determined using inductively coupled plasma optical 

emission spectrophotometry (ICP-OES). Samples and standard reference materials (see below) were 

filtered (0.45 μm) prior to analysis. Analytical ICP-OES results are available upon request.

Sample Preparation and Analysis for Mercury and Selenium

Approximately 40 clams were selected from each collection. The only criterion for selection was 

that the range of sizes (shell length) within this group was representative of the larger collection.

Otherwise, the selection of individuals was random. Selected individuals were grouped according to size 

to form three composites, each containing a minimum of ~1.25 grams wet weight. To meet this 
9

requirement, especially for the smaller clams, the 1-mm size classes were usually combined to form 

broader size classes (within 3–4 mm of each other, as appropriate). Once the composites were formed, 

the clams were dissected as described above, and the soft tissue was placed into preweighed 30-mL 

screw-top polycarbonate vials. These vials were closed and temporarily transferred to a freezer (–20 oC).

The tissue sample was partly thawed and homogenized with a high-speed tissue homogenizer. Once 

homogenized the samples were refrozen (–80 oC), and then freeze-dried. 

Tissue and sediment samples were subsampled and analyzed for total mercury by acid-digestion, 

BrCl oxidation, purge and trap, and cold vapor atomic fluorescence spectrometry according to the U.S. 

Environmental Protection Agency Method 1631, Revision E (2002), and for selenium by acid digestion, 

hydrogen peroxide oxidation, hydride generation inductively coupled plasma mass spectrometry (HGICP-MS) according to a method modified from Liber (2011) and Elrick and Horowitz (1985).

Quality Assurance

All glass and plastic materials used in the collection, preparation, and storage of samples were 

first cleaned thoroughly to remove metal contamination. Cleaning consisted of a detergent wash and 

rinse in deionized water, followed with a 10-percent hydrochloric-acid wash and thorough rinse in 

double-deionized water (approximately 18 mega-ohm [MΩ-cm] resistivity). Materials were dried in a 

dust-free positive-pressure environment, sealed, and stored in a dust-free cabinet. 

Samples prepared for ICP-OES analysis (that is, all elements except Se and Hg) were 

accompanied by procedural blanks and standard reference materials (SRMs) issued by the National 

Institute of Standards and Technology (NIST). Analysis was preceded by instrument calibration, 

followed by quality-control checks with prepared quality-control standards before, during 

(approximately every 10 samples), and after each analytical run. Metal recoveries of sediment digests 

were evaluated with NIST 2709a San Joaquin soils and NIST 2711a Montana II Soil (appendix 1). 

Metal recoveries for soft tissue digests were evaluated with NIST 2976 Mussel Tissue and NIST 1566b 

Oyster Tissue (appendix 2). Results were consistent within methods, and most elements were within the 

ranges of certified values, with the following exceptions. The near-total extraction method recovered on 

average 43 and 38 percent of the Al and 58 and 55 percent of Cr in NIST 2709a and 2711a, respectively. 

Recovery of Pb averaged 60 percent in NIST 2709a. Recoveries for the near-total extraction method 

compared favorably to those reported by NIST for USEPA methods 200.7 and 3050B. Recoveries of 

elements in biological SRMs were consistently greater than 80 percent with a few exceptions. Nickel 

recovery ranged from 69 to 77 percent among the three SRMs (2976, 1566b, and Tort2). Lead averaged

77 percent in SRM 2976. Zinc was not quantified in SRM 1566b due to the high concentrations. The 

lower recovery in SRM 1566b likely reflects poor quantitation of the high Zn concentrations present in 

the samples. 

Quality assurance for Hg and Se methods comprised analyses of sample splits (appendix 3) and 

a variety of standard reference materials (appendix 4). Observed concentrations of reference material 

fell within the range of their certified values (appendix 4).

Method detection limits (MDL) and reporting levels (MRL) for ICP-OES methods were 

determined using the procedures outlined by Glaser and others (1981), Childress and others (1999), and 

U.S. Environmental Protection Agency (2004) (appendix 5). A full quality-assurance/quality-control 

plan is available upon request. 

Salinity

A small volume (approximately 25 mL) of water that had pooled on the surface of the mudflat 

was collected in a polypropylene bottle and returned to the laboratory, where it was measured for 
10

salinity with a handheld refractometer. Additionally, salinity is determined in a small volume 

(approximately 1–2 mL) of bay water that is collected from the body cavity of M. petalum. Salinity of 

the surface water sample and the body water sample consistently agreed within ±2 parts per thousand 

(ppt). 

Other Data Sources

Precipitation data for San Francisco Bay are reported from a station at San Francisco 

International Airport (station identification SFF) and were obtained from the California Data Exchange 

Center (http://cdec.water.ca.gov/). 

Biological Response

Condition Index

The condition index (CI) is a measure of the clam’s physiological state derived from the relation 

between soft tissue weight and shell length and reported as the soft tissue dry weight (in grams) for a 

clam of a particular shell length (in mm). Specifically, for each collection, the relation between the 

average shell length and tissue dry weight of the composites was fit with a linear regression, and from 

that regression, the tissue dry weight was predicted for a normalized shell length of 25 mm. 

Reproductive Activity

A minimum of 10 clams of varying sizes (≥10 mm shell length) were processed for reproductive 

activity concurrent with samples for metal analyses. Clams were immediately preserved in 10-percent

formalin at the time of collection. The visceral mass of each clam was removed in the laboratory, stored 

in 70-percent ethyl alcohol, and then prepared using standard histological techniques. Tissues were 

dehydrated in a graded series of alcohol, cleared in toluene (twice for 1 hour each), and infiltrated in a 

saturated solution of toluene and Paraplast® for 1 hour, and two changes of melted Tissuemat® for 1 

hour each. Samples were embedded in Paraplast® in a vacuum chamber and then thin sectioned (10 μm) 

using a microtome (Weesner, 1960). Sections were stained with Harris’ hematoxylin and eosin, and 

examined with a light microscope. Each individual was characterized by size (length in mm), sex, 

developmental stage, and condition of gonads, thus allowing each specimen to be placed in one of five 

qualitative classes of gonadal development (previously described by Parchaso, 1993). 

Community Analysis

Samples for benthic community analysis were collected with hand-held core 8.5-cm in diameter

and 20-cm deep. Three replicate samples were taken arbitrarily, within a square-meter area, during each 

sampling date.

Benthic community samples were washed on a 500-μm screen, fixed in 10-percent formalin, and 

then later preserved in 70-percent ethanol. Samples were stained with rose bengal solution. All animals 

in all samples were sorted to species level where possible (some groups, such as the oligochaetes, are 

still not well defined in the Bay), and individuals for each species were enumerated. Taxonomic work 

was performed in conjunction with a private contractor familiar with the taxonomy of San Francisco 

Bay invertebrates (Susan McCormick, Colfax, California) (appendix 8). McCormick also compared and 

verified her identifications with previously identified samples.
11

Results

Salinity

Surface-water salinity in the Bay is related to and roughly the inverse of the seasonal weather 

pattern in Northern California, which is characterized by a winter rainy season, defined as months with 

rainfall amounts greater than 0.25 inches (November through April), and a summer dry season (May 

through October). Total precipitation measured at station SFF in 2015 was 9.7 inches with slightly more 

than half of that occurring in December (http://cdec.water.ca.gov/) (fig. 2). Cumulative precipitation in 

2015 was less than half the average annual rainfall of 20 inches during the period of record (1994–2015) 

(fig. 2). Salinity varied between 23 and 30 ppt during 2015 (fig. 3, table 1). Mean annual salinity 

correlated with annual cumulative rainfall (Pearson r = - 0.53; p = 0.01; n = 22), and appears to have 

increased over the period of record (fig. 3). 

Sediments

Metal concentrations in surface sediments from Palo Alto typically display an annual periodicity 

that generally corresponds to seasonal fluctuations in the relative abundance of fine particles (figs. 4–8, 

appendix 1). Thomson-Becker and Luoma (1985) suggested that this intra-annual variation is related to 

changes in the size distribution of sediment particles caused by allocthonous inputs and deposition of 

fine-grained particles in the winter and their subsequent wind-driven resuspension in the summer and 

fall. Because metal concentrations vary as a function of the ratio of surface area to volume of a particle, 

metal concentrations tend to track the percent of fine particles. The seasonal variation in metal 

concentrations in surface sediment suggests that the particle-size distribution within the <100 μm 

sediment fraction varies seasonally. In particular, the concentrations of Al and Fe correlate with the 

abundance of fine particles, reflecting the contribution of clays rich in Al and Fe (fig. 4C). 

Surface sediments from Palo Alto in 2015 contained on average 1.28 percent (by weight) total 

organic carbon (TOC) (table 1). As with metals, TOC varied with the percentage of fine-grained (<100 

μm) sediment particles throughout the year. 

Chromium (Cr) and nickel (Ni) are highly enriched in some geologic formations within the 

watershed. Studies of sediment cores from North San Francisco Bay indicated that concentrations of 

these elements similar to those reported here were derived from natural geologic inputs (Hornberger and 

others, 1999; Topping and Kuwabara, 2003). At Palo Alto, seasonally varying concentrations of Cr and 

Ni in surface sediments may indicate inputs of Cr and Ni bearing minerals from the surrounding 

watershed. In 2015, as in previous years, maximum concentrations coincided with winter/spring 

maxima in fine sediments, consistent with inputs from the surrounding watershed, whereas minimum 

concentrations occurred during the late summer/fall (fig. 5, table 1). However, concentrations of both 

elements typically vary by less than 20 percent. Moreover, identification of inputs is confounded by 

seasonal changes in the particle size distribution of sediments described above. Chromium and Ni 

concentrations have differed between years during the record (p<0.05; ANOVA). For example, Cr was 

relatively high in 2003 and during 2009–2010. In 2015, the respective concentrations of Cr and Ni were

118±4 (mean ±1 standard error of the mean (SEM)) and 102±6. 

Concentrations of Cu and Zn in sediments are shown with sediment guidelines set by the 

National Oceanic and Atmospheric Administration (Long and others, 1995) in figures 6 and 7 and table 

1. Long and others (1995) defined values between ERL (effects range-low) and ERM (effects rangemedian) as concentrations that are occasionally associated with adverse effects on sensitive species (21–

47 percent of the time for different metals). Values greater than the ERM were frequently associated 
12

with adverse effects on sensitive species (42–93 percent of the time for different metals). It is important 

to note, however, that these effects levels were derived mostly from bioassay data and are not accurate 

estimates of site-specific sediment toxicity. For most of the record, Cu concentrations have exceeded the 

ERL (34 mg/kg). In 2015, the average annual copper was 34±2 (SEM) mg/kg, practically equivalent to 

the ERL, as a result of the relatively higher concentrations during the middle part of the year. The 

typical annual pattern was evident: Cu increased during the first half of the year, then declined in the fall 

(fig. 6, table 1). In general, the partial-extractable Cu concentrations correlate with the near-total Cu 

(p<0.001 for the 1994–2015 dataset). The partial extractions represent approximately 42 percent of the 

Cu recovered in the near-total digest. Near-total Zn concentrations were below the Zn ERL (150 mg/kg) 

for much of the record (fig. 7, table 1). Exceedances typically occurred during the winter season. In 

2015, the average Zn concentration was 139±6 mg/kg with a maximum concentration of 161 mg/kg in 

March. 

The annual average of silver extracted from sediments using the partial-extraction method has 

varied from a high of 1.62 mg/kg in 1979 to a low of 0.20 mg/kg in 2008–2009 (appendix 2). In 2015, 

Ag concentrations averaged 0.33±0.04 mg/kg. Like other trace elements, Ag concentrations have 

displayed a seasonal pattern over the record (fig. 8, table 1). In 2015, annual maxima were observed 

during February and March (0.44–0.49 mg/kg, and annual minima occurred from September to 

December (0.10–0.26 mg/kg). 

Mercury concentrations in sediment from Palo Alto during 2015 averaged 0.44 mg/kg (table 1), 

which was slightly elevated compared to the previous four years (fig. 9). Concentrations in February 

(0.61 mg/kg) and in December (0.67 mg/kg) were notable for being among the highest concentrations 

recorded at the site. These concentrations appear to be at the upper range of concentrations typical for 

South Bay sediment (Davis and others, 2012). 

Selenium concentrations in 2015 ranged modestly from 0.30 mg/kg (December) to 0.44 mg/kg

(September), and averaged 0.36 mg/kg (fig. 9, table 1). Concentrations in 2015 were comparable to 

those of the previous year. Sedimentary Se hasn’t exhibited a sustained temporal trend over the period 

of the record. During this time, Se concentrations have alternated from relatively high (2004, 2006, 

2008, and 2011) to relatively low (2005, 2007, 2009–2010, 2012, and 2014–2015). 

Clam Tissue

Metal concentrations in the soft tissues of Macoma petalum reflect a combination of metal 

exposures from water and food, and the diluting and concentrating effects of gaining and losing tissue 

mass associated with annual growth and reproductive cycles. Exposures to Cu and Ag at Palo Alto are 

of special interest because of the high tissue concentrations observed at this site in the past (figs. 10 and 

11, appendix 7). During 1977–1990, the ranges in annual concentrations of Cu and Ag were 35–287 

mg/kg and 7.7–106 mg/kg, respectively. Since 1990, concentrations have been considerably lower, 24–

71 mg/kg for Cu and 1.8–7.5 mg/kg for Ag. Concentrations have been particularly low and stable since 

1997, except for a 2-year period in 2006–2007 when concentrations increased modestly. Annual mean 

concentrations of Cu and Ag for 2015 were 43±7 mg/kg and 3.3±0.6 mg/kg, respectively (table 2). 

Intra-annual variations in Ag and Cu concentrations in clam soft tissues display a consistent 

seasonal signal characterized by fall/winter maxima and spring/summer minima. The amplitude of this 

seasonal cycle varies from year to year. For example, the winter maxima and the magnitude of seasonal 

Ag and Cu concentrations during 1994–1997 and in 2007 were large relative to other years (figs. 12 and

13). In 2015, both Cu and Ag concentrations followed a typical seasonal pattern that was of similar 

magnitude as that observed in 2007. These patterns most likely reflect the interaction between the 

exposure regime at the site and the annual growth and reproductive cycles of M. petalum (Cain and 
13

Luoma, 1990). The latter can largely account for intra-annual variability in tissue metal concentrations 

during periods of relatively stable metal exposures. For example, over the period of 1994 to 2015, the 

seasonal variations of Cu and the CI varied inversely of one another and were of similar magnitude, 

suggesting that variations in tissue weight driven by growth and reproduction highly influenced the 

tissue Cu concentrations (fig. 12C). 

As with Cu and Ag, tissue concentrations of Cr (fig. 14, table 2), Ni (fig. 15, table 2), and Zn 

(fig. 16, table 2) also exhibited annual cycles of variable magnitude throughout the record. None of 

these elements exhibit a clear temporal trend (either downward or upward) in concentration. In 2015, 

the annual average Cr, Ni, and Zn concentrations were 2.6, 5.6, and 195 mg/kg, respectively. Wellise 

and others (1999) observed that intra-annual and inter-annual patterns of Cr, Ni, and Zn in M. petalum at 

Palo Alto were generally similar to those observed near the San Jose/Santa Clara Water Pollution 

Control Plant, indicating that regional-scale processes may be more important than treatment plant 

inputs in controlling the bioavailability of these elements. 

The average Hg concentration in M. petalum in 2015 was 0.43 mg/kg (fig.17, table 2). Intraannual variation of Hg in 2015 displayed the typical pattern of fall/winter maxima and spring/summer 

minima. The maximum concentrations of Hg in M. petalum (January and September) did not coincide 

with maximum total sedimentary Hg concentrations (February and December). Although Hg 

concentrations increased in 2015 relative to the previous four years, a long-term trend in Hg 

concentration is not evident (fig. 17A). 

Selenium concentrations in M. petalum averaged 4.49 mg/kg in 2015 (table 2). An annual cycle 

of moderate magnitude was displayed with the highest concentrations in January (5.07 mg/kg) and the 

following September and December (4.93 and 4.63 mg/kg, respectively; fig. 18, table 2). Although peak 

concentrations of Se have been lower during 2012 to 2015 than most previous years, a long-term trend 

is not evident. 

Data on the condition index for M. petalum at Palo Alto extends back to 1988 (fig. 19, table 2). 

As previously discussed, the data fluctuate seasonally in relation to growth and reproductive cycles, and 

annual cycles differ in magnitude. Condition index values typically increase to a maximum in the spring 

(pre-spawning period) then taper off throughout the year (fig. 19C). The seasonal variation of CI in 

2015 was typical for the record, and the annual average CI (134 mg) was consistent with values 

observed since 2007. The maximum CI in May (228 mg) coincided with the minima for most of the 

metals concentrations in M. petalum in 2015, and the minimum CI (65 mg in February) coincided with 

the maxima for most of the metal concentrations in M. petalum. 

Reproduction of Macoma petalum

Previous studies suggested that reproduction in M. petalum is affected by Ag (Hornberger and 

others, 1999; Shouse and others, 2003). The time series of reproductive activity (fig. 20) shows that 

reproductive activity was lowest with periods of reproductive inactively during 1974–1983, coincident 

with the period of highest Ag and Cu exposure. As metal exposures declined during the 1980s and into 

the early 1990s, reproductive activity increased. Data from 2015 show that M. petalum continues to be 

highly reproductive relative to the 1970s with a relatively high percentage of the animals being 

reproductively active in any given sample. A closer look at the last five years of data (2011–2015) 

demonstrates the seasonality of reproduction in M. petalum (fig. 21, table 3). Reproductive activity 

commences in the fall and concludes the following spring. 
14

Benthic Community

Estimates of species diversity and total animal abundance are simple metrics that are used in 

assessing environmental stress on biological communities. Species diversity at the Palo Alto site, as 

estimated by a time series of number of species was at a minimum in 1998, trended upward through 

2012, and has shown a slight decline since its peak in 2012 (fig. 22). Total animal abundance has varied 

significantly during the sampling period (fig. 23). The difficulty with these types of metrics is that they 

do not consider the possibility that one species can take the place of another or that high abundance is 

based on one species. Depending on the characteristics of a species new to the community or newly 

dominant in the community, the community structure and function may change as a result of this change 

in species composition or dominance. The details of changes in species composition are important 

because they may reflect the relative ability of species to accommodate environmental stress and 

redistribute site resources. In general, the species composition at the study site has changed little since 

1998, although there have been seasonal eruptions of several species in some years. 

Three common bivalves (Macoma petalum, Mya arenaria, and Gemma gemma) have not shown 

any consistent trend over the 42-year period from 1974 to 2015 (figs. 24–26). Significant seasonal and 

inter-annual variability has been displayed in species abundances for all species found at the Palo Alto 

site. The three common bivalves illustrate this variability well. Gemma gemma has been particularly 

volatile since 2005. Gemma gemma abundance dropped to near zero in late fall 2007, took three years to 

recover to previous average densities, and then continued this abundance through 2015. 

Six species have shown trends in their abundance since the 1970s, and these trends continued 

through 2015. The first species, Ampelisca abdita, is a small crustacean that lives above the surface of 

the mudflat in a tube built from selected sediment particles. A. abdita showed a general decline in 

abundance (fig. 27) after 1998 and mostly low abundances persisted through 2014. In 2015, A. abdita

showed an order of magnitude increase in abundance. The second species to show a significant trend is 

the small polychaete worm Streblospio benedicti, which also builds a tube above the surface of the 

mudflat. S. benedicti abundance has declined through the study years and, over the past 7 years, the 

species has maintained a seasonal pattern of increasing spring abundance followed by a fall/ winter 

decline throughout the study (fig. 28). The abundance of the small burrowing crustacean Grandiderella 

japonica, a deposit feeder, became more seasonally consistent after 2000 (fig. 29), with particularly low 

abundances in 2006, 2007, and 2011. This species has shown a consistent seasonal peak in abundance in 

the fall since 1999 with the exception of 2011. Neanthes succinea, a burrowing polychaete that feeds on 

surface deposits and scavenges for detrital food, showed large seasonal fluctuations in abundance 

throughout the study (fig. 30) and like other species its abundance declined in 2011 and remains in low 

numbers in 2015. Two species showed an increase in abundance within the time series. The first was the 

polychaete worm Heteromastus filiformis (fig. 31), a burrowing, subsurface-deposit-feeding species that 

lives deep in the sediment (usually 5–20 cm below the surface of the mudflat). Abundance increased 

sharply in 1985 and then partly receded in the late 1980s. Abundance remained higher than in the late 

1970s until 2008, when there was a large decline in H. filiformis abundance (fig. 31). H. filiformis

abundance increased slightly after 2010. Abundance data from the 1980s indicate that this is a species 

that increases slowly, possibly because of their egg-laying mode of recruitment. The second species 

showing an increase was Nippoleucon hinumensis, a small, burrowing, surface-deposit-feeding 

crustacean, which appeared in the dataset in 1988 (fig. 32) following its introduction into the bay in 

1986 (Cohen and Carlton, 1995). A complete list of the benthic species found at the Palo Alto site in the 

year 2015 is shown in appendix 8. The benthic species name changes (as of 2015) for the species listed 

in appendix 8 are shown in appendix 9. 
15

A sudden drop in animal abundance was observed in February 2008. Very few animals were 

found at the site, and the mudflat community was evidently stressed by some event between the January 

and February sampling. Possible causes of the stress include sedimentation or freshwater inundation. 

There was a large storm on January 25, 2008, with rainfall rates exceeding 0.5 cm/hr for more than half 

the day, including during the low-tide period. No obvious changes in the sediment surface were 

observed, but sediment changes can occur and be incorporated quickly in this tidal environment. Other 

possible causes of benthic community death or exodus include a toxic event or anoxia. It is unlikely that 

either of these occurred, because M. petalum were present in the deep sediment in February 2008, and 

animals were found again at the site in March 2008. This would not happen with toxicity or anoxia. The 

timeline for recovery from anoxia can be estimated on the basis of observations following an anoxic 

event at this site in 1975. Macroalgae were deposited on the mudflat surface and began to decay, and the 

resulting bacterial consumption of oxygen led to anoxia. The benthic community took many months to 

recover from this anoxic event. Animals that returned after the disturbance in 2008 include those species 

with pelagic larvae and mobile adults, as would be expected. Nonmobile brooders returned to the site in 

2009, concurrent with an increase in abundance of the brooding clam G. gemma and the brooding 

polychaete Streblospio benedicti. This trend continued into 2015, when brooder species were more than 

half of the top 10 most abundant species, while oviparous and spawner species made up the rest. 

Multivariate analyses of population data of the dominant species with environmental parameters 

did not reveal any relations, except with the concentration of Ag and Cu in the sediment and in the 

tissue of M. petalum (using data reported by David and others, 2002). Therefore, this update will 

consider only those metals. Metal concentration and abundance of species with the most susceptible 

mode of feeding and reproduction will be compared over the period of the study. One such susceptible 

species, the worm H. filiformis, increased in abundance with the decrease in Ag and Cu until 2008 (fig. 

31). This was of interest because H. filiformis has continual tissue contact with the sediment at the 

exterior of its body, as well as within its body, as a result of its lifestyle of burrowing through the 

sediment and consuming a diet of mud and organic particles. In addition, this is one of the few species 

in the present community that reproduces exclusively by laying its eggs in the sediment. The larvae 

hatch after 2 or 3 days and spend a very short period (2–3 days) in the plankton before settling back to 

the mud as juvenile worms (Rasmussen, 1956). The short planktonic period limits the species’ speed of 

expansion into new areas. The authors hypothesize that once a few individuals successfully arrived at 

the study site, H. filiformis increased in abundance because either the adult worms or the eggs found the 

environment agreeable. This species is not likely to move into an area quickly after an environmental 

stressor because of its mode of reproduction and short planktonic larval period. A large spike in H. 

filiformis abundance was observed in January 2008 because of the settling of larvae, but these larvae did 

not survive the event that occurred before the February sampling. So far, the species has not returned in 

high numbers to the study site. The dynamics of recovery for this species will continue to be monitored 

closely.

Two species have shown the opposite trend of H. filiformis, the crustacean A. abdita (fig. 27)

and the worm S. benedicti (fig. 28) have declined in abundance coincident with the decline in metals. 

These species have very similar life-history characteristics that make them less susceptible to high Ag 

and Cu concentrations in sediment. Both species live on the surface of the sediment in tubes that are 

built from sediment particles. They feed on particles in the water column or on particles that have settled 

to the sediment surface, brood their young, and produce young that are capable of either swimming or 

settling upon hatching. These opportunistic characteristics make these species ideal for invading a 

disturbed or stressed environment; thus, they are capable of rapid increase in population size and 

distribution. It is not surprising that both species immediately responded to the near-empty community 
16

in February 2008 and have subsequently declined (figs. 27 and 28). This abundance pattern is consistent 

with what is expected of an opportunistic species, confirming both their tolerance to elevated metals as 

well as an inability to out-compete less opportunistic diverse communities in non-stressed conditions. 

Other species share the characteristics highlighted in our discussion of H. filiformis, S. benedicti, 

and A. abdita; the species with similar characteristics have been combined into plots that examine the 

percent of abundance represented by each feeding and reproductive mode (figs. 33–36). Because the 

natural spatial variability (that is, the large standard deviations around the monthly means) and seasonal 

variability of invertebrate abundance can be quite large, the average percentages for the month of 

August of each characteristic reproductive and feeding mode are shown in figures 33–36. To interpret 

these plots, the life-history characteristics must first be examined to determine if there is some 

mechanism by which this organism could be responding to a decrease in Ag or Cu in the environment. It 

is likely that Ag, but probably not Cu, adversely affected reproduction of all animals (Hornberger and 

others, 2000b). If species with pelagic larvae were transported into the area they did not survive to 

dominant the community. Species having oviparous and mixed (species capable of oviparity and 

brooding) reproductive modes (Ahn and others, 1995; Hornberger and others, 2000b) are worth 

examining in more detail. The gradual increase in abundance of this group through 1983 occurred 

concurrently with the gradual reduction of metals in the environment during that time. In the present 

environment, with much lower metal concentrations, these species respond to a different variety of 

stresses, and the percentage of brooding and oviparous individuals in the community reflects those 

stresses (figs. 33 and 34). Although the percentage is variable, the brooders plus oviparous individuals 

has never been as high as it was in the early 1970s. The authors interpret this as being a reflection of the 

general health of the benthic environment. In a similar manner, we can examine the feeding modes of 

the majority of the individuals (figs. 35 and 36). High concentrations of either Cu or Ag in the sediment 

are unlikely to be healthy for species that ingest the sediment in order to consume the interstitial and 

attached carbon; thus, it is reasonable to expect species that consume particles from the water column to 

be more protected from the contaminants in the sediment. Filter feeding species are usually the 

dominant group throughout the data set, and the subsurface deposit feeders are the group that shows the 

largest increase in dominance after the 1970s. This is consistent with the conceptual model posed here. 

The change in function of the benthic community over time can be examined by ranking the top 

10 species by abundance and plotting the log (n + 1) of mean abundance against the rank of each 

species. The plot for 2015 (fig. 37) is indicative of a healthy benthic community with species 

dominance, as revealed by abundance, not showing large differences among the top 10 species. An 

examination of similar plots for August of three hydrologically dry years during this study (1977, 1989, 

and 2002) shows that the shape of the curve has changed greatly and that the 2015 curve is similar to 

that seen in 1989. The figure shows a community that was, with the rest of the species having similar 

abundances, heavily dominated by three species in 1977, 1989, and 2015, versus a community with one 

dominant species in 2002. Although G. gemma is the most dominant species in all years except 1989; in 

2015, the graph shows a smooth downward slope showing a more homogenized decrease in species 

abundance. The 1977 community plot is the most extreme, with three species dominating the 

community and the remainder having similar but relatively low abundances. It is informative to examine 

the rank-abundance plots within the context of the life-history characteristics of each species to 

determine if shifts in plot shape coincide with a shift in community structure and function that might be 

indicative of a healthier environment. Two critical life history characteristics are shown: feeding mode 

in figure 38 and reproductive mode in figure 39. The 1977 community was dominated by filter feeding 

species (species that consume particles in the water column), mixed feeders (species that have the option 

of either filter feeding or feeding on the sediment surface), and two species that feed on food particles 
17

on the sediment surface. In 1989, the species composition had shifted such that filter feeding species, 

subsurface deposit and surface deposit feeding species (those that ingest sediment and strip the food off 

of the sediment in their gut) dominated the community. In 2002, a shift was observed towards species 

that could either filter feed or deposit feed (mixed feeders) and those species that feed on subsurface 

sediment. The most recent data (2015) show the community to be similar to that of 1989, with the 

composition having shifted to that of filter feeding species, subsurface deposit and surface deposit 

feeding species. Over the period of this study, a shift has occurred from a community dominated by 

species that feed either in the water column or on recently settled food particles on the sediment surface 

to a mixed community of species that feed directly on the subsurface sediment, those capable of feeding 

in the water column, and those feeding on the sediment surface. The species that returned following the 

defaunation event in January/February 2008 have maintained this pattern. Thus, it is unlikely that any 

sediment-borne pollutant caused the collapse of the community in early 2008. 

An examination of these rank-abundance plots using reproductive mode as the descriptor for 

each point is equally informative (fig. 39). The dominant species in 1977 were species that brood their 

young and release fully functional juveniles into the environment. In 1989, there were still several 

brooders, but there were also two species that lay their eggs in the sediment. Although brooding species 

remain the most abundant species for all years, species that spawn their gametes into the water column 

in combination with those that lay eggs in the sediment (oviparous) have the highest presence. It is 

possible that some of the metal contaminants found in the sediment in the 1970s at this location limited 

the success of species that consumed the sediment for food, laid eggs in the sediment, or depended on 

water-borne larvae to repopulate the community. Interestingly, the reproductive mode of most species 

present in 2015 is brooding with some egg laying (oviparous) and spawning species

Summary 

Long-Term Observations

Since 1974, USGS personnel have monitored and conducted basic research on the benthic 

sediments and biological community in the vicinity of the discharge of the Palo Alto Regional Water 

Quality Control Plant (PARWQCP). The time series presented here update previous findings (for 

example, Hornberger and others, 2000a; Luoma and others, 1991, 1995a, 1996; Moon and others, 2005; 

Shouse and others, 2003, 2004; Thompson and others, 2002; Cain and others, 2006; Dyke and others, 

2011, 2012) with additional data from January 2015 through December 2015 to create a record spanning 

41 years. This long-term dataset includes sediment chemistry and tissue concentrations of metals (1977–

2015 for Cu and Ag, 1994–2015 for other metals), condition index (1988–2015) and reproductive 

activity in M. petalum, and population dynamics of benthic invertebrate species (1974–2015). This time 

series encompasses the period when exceptionally high concentrations of Cu and Ag were found in M. 

petalum (1970s and early 1980s) and the subsequent period when those concentrations declined. The 

sustained record of biogeochemical data at this site provides a rare opportunity to examine the 

biological response to metal contamination within this ecosystem. 

Studies during the 1970s showed that sediments and M. petalum at the Palo Alto site contained 

highly elevated levels of metals, especially Ag and Cu, as a result of metal-containing effluent being 

discharged from the Palo Alto Regional Water Quality Control Plant (PARWQCP) to South San 

Francisco Bay. In the early 1980s, the point-source metal loading from the nearby PARWQCP was 

significantly reduced as a result of advanced treatment of influent and source mitigation. Coincident 

with declines in metal loadings, concentrations of metals in the sediment and in the clam M. petalum

(serving as a biomonitor of metal exposures) also declined, as previously described by Hornberger and 
18

others (2000b). Inter-annual trends in clams and sediments were highly correlated with Cu loadings 

from PARWQCP (concurrent loading data for Ag were not available). Metal levels in sediments and 

clams responded relatively quickly to changes in metal loading; the reduction in metal loadings by the 

PARWQCP resulted in a reduction in metal concentrations in both the sediment and M. petalum within 

a year (Hornberger and others, 2000b). 

Biological responses to metal inputs to South San Francisco Bay were assessed at different 

levels of organization. These responses are interpreted within the appropriate temporal context. Because 

metal exposures were already high when the study began, interpretations are based on observed changes 

in biological attributes as metal inputs declined. In general, discernable responses at the organism level 

(that is, reproductive activity, a manifestation of a cellular or physiological change) to metal exposure 

may occur within a relatively short time (for example, at intra- and inter-annual time scales as 

previously exposed individuals recover and successive cohorts become established), whereas population 

and community level responses take longer to develop. Stable changes in the benthic community may 

take a relatively long period of time to be expressed because of the normally high degree of intra-annual 

variability of benthic community dynamics, which reflects the cumulative response to natural and 

anthropogenic disturbances. It is therefore critical that sampling frequency and duration be conducted at 

temporal scales appropriate to characterize the different biological responses. 

During the first 10 years of this study, when the metal concentrations were high and declining, 

the benthic community was largely composed of nonindigenous, opportunistic species that dominated 

because of their ability to survive the many physical disturbances on the mudflat (Nichols and 

Thompson, 1985a,b). These disturbances included sediment erosion and deposition and aerial exposure 

at extreme low tides, as well as less well defined stresses. The possible effects of metal exposure as a 

disturbance factor were not considered in the analyses by Nichols and Thompson because the decline in 

metal concentrations in M. petalum and sediment had just begun. 

However, data collected throughout the period of declining metal exposure have revealed 

biological responses to this metal decline. Reproductive activity improved within a year or two of 

reduced metal exposure, and responses at the population and community levels were observed 

afterward. Identification of these responses was possible because the frequency of sampling allowed 

long-term trends related to metal contamination to be identified within the context of repeating seasonal 

cycles and unrelated intra-annual variation. Decreasing particulate concentrations of trace metals in the 

local environment have improved the condition of resident populations of invertebrates. 

The dramatic decline in the benthic community in early 2008 did not appear to be related to 

metals, but instead may have been the result of a natural stressor, such as a sedimentation or freshwater 

event. The composition of the benthic community supports that supposition. Mobile animals such as M. 

petalum that were capable of burrowing down to avoid the stressor probably did so, but many other 

species either relocated or were killed. This natural disturbance gives scientists the opportunity to 

observe mudflat community recovery from a natural stressor and to compare this recovery to that 

observed during the long-term decline in metals. Long-term shifts in species abundance at Palo Alto 

have been interpreted to be a response to decreasing sediment contaminants. These community changes 

have included a shift from species that live on the surface, filter food out of the water column or 

consume particles on the sediment surface, and brood their young, to a community dominated by 

species that live on and below the surface, consume the sediment directly to harvest food particles, and 

spawn and lay eggs in the sediment. The 2008–2015 data reveal a community that had a short-term 

physical stressor but not one that was subject to unhealthy sediment. This “natural experiment” has 

given USGS scientists a great opportunity to test various hypotheses on the benthic community response 
19

to different stressors. Future data will further refine the understanding of the response of this benthic 

community to natural and anthropogenic. 

The ecology of the Palo Alto mudflats is part of the larger South San Francisco Bay, which has 

been undergoing some changes in recent years. During 1999–2005, USGS scientists noticed an increase 

in phytoplankton biomass in the southern bay. Sampling in the deeper water of the southern bay showed 

that the bivalves were mostly absent from the system during this increase in primary production. Cloern 

and others (2007) indicate that the cause of the decline in bivalves was an increase in fish predators 

resulting from increased offshore upwelling activity. The higher reproductive success of demersal fish, 

crabs, and shrimp during this period resulted in a higher number of juveniles moving into the South San 

Francisco Bay to grow. Since 2005, scientists have seen the large bivalve populations fluctuate more 

than in previous years, and these fluctuations have been reflected in changes in phytoplankton biomass 

in the system (primarily through an increase in phytoplankton biomass in late summer and fall). The 

value of these findings in greater South San Francisco Bay to this study is twofold. First, it reinforces 

the importance of the benthic community’s impact on ecosystem function. Second, it shows that the 

high intertidal community at the Palo Alto site has not been demonstrably affected by these greater 

South San Francisco Bay influences during these years. This finding solidifies the authors’ confidence 

that the changes observed in the benthic community are in large part due to local factors. 

2015 Observations

Throughout 2015, Cu and Ag concentrations in sediments and soft tissues of the clam, M. 

petalum, remained representative of the concentrations observed since 1991, following the significant 

reductions in concentrations during the 1980s that coincided with reductions in the discharge of these 

elements from PARWQCP. Since 1991, annual mean Cu and Ag concentrations have fluctuated 

modestly and without any extended trends. This is also true for other elements. For example, 

sedimentary selenium (Se) concentrations have been variable from year to year and showed no sustained 

temporal trend. Selenium concentrations in surface sediment declined in 2009–2010 from the record 

high concentrations observed in 2008, increased in 2011, and subsequently (2012–2015) decreased to 

about half the annual average observed in 2008. In another example, annual average concentrations of 

Cu and Ag in M. petalum were relatively low from 1997 to 2005, increased notably in 2006–2007, 

returned to 1997–2005 levels during 2008–2014, and in 2015 increased again to levels comparable to 

2006–2007. Silver annual averages in M. petalum also were slightly greater in 2015 compared to the 

previous seven years. However, the most recent results (2015) show that Ag and Cu in M. petalum are 

only 3 percent and 15 percent, respectively, of the maximum values observed during 1978–1980. Since 

1994, the magnitude of the annual growth and reproductive cycle of M. petalum appears to influence the 

modest inter-annual variation in elemental tissue concentrations. Concentrations of Ag and Cu in 

sediments in 2015 were 20 percent and 40 percent, respectively, of the record high concentrations 

observed in 1979. Inter-annual variation in Cu and Ag in M. petalum from 1991 to 2006 did not 

correlate with discharge of Cu and Ag from PARWQCP (Lorenzi and others, 2007), indicating that, as 

with other elements of regulatory interest, including Cr, Ni, and Zn, regional-scale factors now largely 

influence sedimentary and bioavailable concentrations (see, for example, Luoma and others, 1998). 

Abiotic factors that affect the seasonal and year-to-year patterns in sedimentary and tissue 

concentrations may include precipitation, nonpoint-source runoff, cycling of legacy contamination, 

accelerated erosion of salt marsh banks in recent years, and periods of accretion and erosion of sediment 

on the mudflat. 

In 2015, individual and community-level metrics did not exhibit any obvious signs of metal 

stress. Recovery of reproductive activity in M. petalum following the decline in metal exposures has 
20

been sustained. The species abundance data and the constancy of functional groups within the benthic 

community continues to show signs of a community that has recovered from metal stress and has 

stabilized. 

Value of Long-Term Monitoring

This study highlights the importance of long-term ecosystem monitoring. Often, antecedent data 

are not available to evaluate ecological responses to contaminants. However, long-term studies may be 

able to separate contaminant-influenced biological responses from those related to natural processes and 

other potential stressors. Such was the case in this study wherein the linkage between metal exposure 

and biological effects was established by examining long-term biological responses at different levels of 

organization (individual, population, community) relative to the mitigation of metal loadings from a 

point source. The decadal time series produced during the course of sustained efforts at the Palo Alto 

site have made it possible to describe trends, identify previously undocumented phenomena, and pose 

hypotheses that have guided past detailed explanatory studies and can guide future studies. Monitoring 

studies cannot always unambiguously determine the causes of trends in metal concentrations or benthic 

community structure. The strength and uniqueness of this study is the integrated analysis of metal 

exposure and biological response at intra- and inter-annual time scales over multiple decades. Changes 

and trends in community structure that may be related to anthropogenic stressors, as was seen in this 

study, can be established only with a concerted and committed effort of sufficient duration and 

frequency of sampling. Such rare field designs allow biological responses to natural stressors to be 

characterized and separated from those stressors introduced by humans. Through interpreting the timeseries data, it has been possible to separate anthropogenic effects from natural annual and inter-annual 

variability. The data from the recent record (that is, within the past decade) with indicators of metal 

contamination, physiological status of an indicator species (M. petalum), and benthic community 

structure increasingly appear to be indicative of an integrated regional ecological baseline. Changes are 

occurring in the South San Francisco Bay watershed. For example, the South Bay Salt Ponds 

Restoration Program has been implemented with unknown implications (positive or negative) for all of 

South San Francisco Bay. Nanomaterials, many of which include metal-based products in forms for 

which environmental scientists and regulators have little or no experience, are being used in an 

increasing number of common consumer products. The long-term, detailed, integrated ecological 

baseline that has been established at this sampling site will be uniquely valuable in assessing the 

response of the environment as human activities in the watershed continue to change. 

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Rygg, B., 1985, Effect of sediment copper on benthic fauna: Marine Ecology Progress Series, v. 25, p. 

83–89. 

San Francisco Estuary Institute, 1997, RMP, regional monitoring program for trace substances; 1996: 

Richmond, Calif., San Francisco Estuary Institute, 349 p. 

Shouse, M.K., 2002, The effects of decreasing trace metal concentrations on benthic community 

structure: San Francisco, Calif., San Francisco State University, M.S. thesis, 177 p. 

Shouse, M.K., Parchaso, F., and Thompson, J.K., 2003, Near-field receiving water monitoring of 

benthic community near the Palo Alto Water Quality Control Plant in South San Francisco Bay; 

February 1974 through December 2003: U.S. Geological Survey Open-File Report 2003–224, 39 p. 

Shouse, M.K., Parchaso, F., and Thompson, J.K., 2004, Near-field receiving water monitoring of 

benthic community near the Palo Alto Water Quality Control Plant in South San Francisco Bay; 

February 1974 through December 2003: U.S. Geological Survey Open-File Report 2004–1210, 39 p. 

Simon, T.P., 2002, Biological response signatures: Boca Raton, Fla., CRC Press, 608 p. 

Thompson, J.K., and Parchaso, F., 2012, Benthic invertebrate community assessment as a 

phytoplankton consumer and fish and bird prey source before and after the start of the restoration: 

South Bay Salt Pond Restoration Project Cooperative Agreement #2009-0211, 90 p. 

Thompson, J.K., Parchaso, F., and Shouse, M.K., 2002, Near-field receiving water monitoring of 

benthic community near the Palo Alto Water Quality Control Plant in South San Francisco Bay; 

February 1974 through December 2000: U.S. Geological Survey Open-File Report 02–394, 117 p. 

Thomson, E.A., Luoma, S.N., Johansson, C.E., and Cain, D.J., 1984, Comparison of sediments and 

organisms in identifying sources of biologically available trace metal contamination: Water Research, 

v. 18, p. 755–765. 

Thomson-Becker, E.A., and Luoma, S.N., 1985, Temporal fluctuations in grain size, organic materials 

and iron concentrations in intertidal surface sediment: Hydrobiologia, v. 129, p. 91–109. 

Topping, B.R., and Kuwabara, J.S., 2003, Dissolved nickel and benthic flux in south San Francisco 

Bay; a potential for natural sources to dominate: Bulletin of Environmental Toxicology and 

Chemistry, v. 71, p. 46–51. 

U.S. Environmental Protection Agency, 2002, Method 1631, Revision E—Mercury in Water by 

Oxidation, Purge and Trap, and Cold Vapor Atomic Fluorescence Spectrometry: Washington, D.C., 

U.S. Environmental Protection Agency, EPA–821–R–02–019, 38 p. 

U.S. Environmental Protection Agency, 2004, Revised assessment of detection and quantitation 

approaches: Washington, D.C., U.S. Environmental Protection Agency, EPA–821–B–04–005, 254 p. 

Wang, W., and Fisher, N.S., 1999, Delineating metal accumulation pathways for marine invertebrates: 

Science of the Total Environment, v. 237, p. 459–472. 
24

Weesner, F.M., 1960, General zoological microtechniques: Baltimore, Md., The Waverly Press, Inc., 

230 p. 

Wellise, C., Luoma, S.N., Cain, D.J., Brown, C., Hornberger, M., and Bouse, R., 1999, Near-field 

receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo 

Alto and San Jose/Sunnyvale Water Quality Control Plants in South San Francisco Bay; 1998: U.S. 

Geological Survey Open-File Report 99–455, 101 p. 
25

Figure 1. Location of the Palo Alto sampling site in South San Francisco Bay, Calif. (A) Sampling area within the 

greater San Francisco Bay region. (B) The intertidal mudflats are shaded light blue, subtidal in dark blue, and 

marshland/brackish water in green/brown. The benthic community and M. petalum and sediments points make up 

the Palo Alto sampling site. The San Jose sampling site (inactive) is also shown for reference. (C) Effluent from the 

Palo Alto Regional Water Quality Control Plant (red thumbtack, insert B) is discharged by way of underground pipe 

(dashed red line) until it reaches the mouth of a small channel that connects to the intertidal mudflat approximately 

1 kilometer northwest of the sampling sites. 
26

0

2

4

6

8

10

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

Precipitation (inches)

Month Total Cumulative

Year

1995 2000 2005 2010 2015

Totoal Annual Precipitation (inches)

0

5

10

15

20

25

30

35

Figure 2. Precipitation recorded at San Francisco WB AP in San Mateo County, CA. Top panel shows the 

monthly and cumulative precipitation in 2015. The bottom panel shows the total annual precipitation for the period 

1994–2015. The station (identification SFF) is operated by the National Weather Service.
27

Jan

Feb

March

April

May

June 

July

Aug.

Sept.

Oct.

Nov.

Dec.

Salinity (‰)

0

5

10

15

20

25

30

35

1994

1996

1998

2000

2002

2004

2006

2008

2010

2012

2014

2016

Salinity (‰)

0

5

10

15

20

25

30

35

Figure 3. Surface-water salinity in parts per thousand (ppt) at the Palo Alto site, Calif., 1994–2015. The top panel 

illustrates seasonal variation as the monthly averages (±1 std, n = 21), and the bottom panel shows individual 

monthly data (dots) and the running average (solid line) indicating the long-term pattern. 
28

 

 2011 2012 2013 2014 2015 2016

Aluminum & Iron (percent dry weight)

0

2

4

6

8

10

Percent <100 m

0

20

40

60

80

100

199419961998200020022004200620082010201220142016

Aluminum & Iron (percent dry weight)

0

2

4

6

8

10

Percent <100 m

0

20

40

60

80

100

Month

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Percent <100 m

0

20

40

60

80

100

Aluminum & Iron (percent dry weight)

0

2

4

6

8

10

A

C

B

Percent ≤100 μm Percent ≤100 μm Percent ≤100 μm

Figure 4. Aluminum, iron, and silt/clay in sediments, Palo Alto, Calif., 1994–2015. (A) Percent aluminum (), 

iron () (extracted by near-total digest), and percent of sediments as silt/clay ≤100 μm (). Data on percent of 

sediment as silt/clay for 2004 contain unquantifiable biases due to errors in sample processing and, therefore, have 

been censored. (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples collected from 

1994–2015, illustrating the general seasonal variation in Al, Fe, and percent fine sediments. Collections are not 

made in July, August, and November. The error bar is the standard error of the mean.
29

19941996199820002002200420062008201020122014

Cr and Ni in sediment (mg/kg)

0

50

100

150

200

2010 2011 2012 2013 2014 2015

Cr and Ni in sediment (mg/kg)

0

50

100

150

200

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Cr and Ni in sediment (mg/kg)

0

50

100

150

200

Figure 5. Chromium and nickel in sediments, Palo Alto, Calif., 1994–2015. (A) Concentrations of chromium (Cr) 

( ) and nickel (Ni) ( ) extracted by near-total digest in milligrams per kilogram (mg/kg). (B) Data for the past 5 

years (2011–2015). (C) The monthly mean of all samples collected from 1994–2015, illustrating the general 

seasonal variation in Cr and Ni. Collections are not made in July, August, and November. The error bar is the 

standard error of the mean.

A

C

B
30

2011 2012 2013 2014 2015 2016

Cu in sediment (mg/kg)

0

20

40

60

ERL=34 mg/kg

199419961998200020022004200620082010201220142016

Cu in sediment (mg/kg)

0

20

40

60

80

260

280

300

ERM=270 mg/kg

ERL=34 mg/kg

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Cu in sediment (mg/kg)

0

20

40

60

Figure 6. Copper in sediments, Palo Alto, Calif., 1994–2015. (A) Near-total ( ) and partial-extractable () 

copper in milligrams per kilogram (mg/kg). (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all 

samples collected from 1994–2015, illustrating the general seasonal variation in Cu. Collections are not made in 

July, August, and November. The error bar is the standard error of the mean. The effects range-low (ERL) is the 

concentration below which the expected incidence of adverse effects is low (9 percent). The effects range-median

(ERM) is the concentration above which the expected incidence of adverse effects is high (84 percent).

A

B

C
31

2010 2011 2012 2013 2014 2015

Zn in sediment (mg/kg)

0

50

100

150

200

250

ERL = 150 mg/kg

Regional 

Background = 75 mg/kg

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Zn in sediment (mg/kg)

0

50

100

150

200

250

19941996199820002002200420062008201020122014

Zn in sediment (mg/kg)

0

50

100

150

200

250

300

350

400

450

500

ERM = 410 mg/kg

ERL = 150 mg/kg

Regional 

Background = 75 mg/kg

Figure 7. Zinc in sediments, Palo Alto, Calif., 1994–2015. (A) Near-total ( ) and partial-extractable () zinc in 

milligrams per kilogram (mg/kg). (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Zn. Collections are not made in July, 

August, and November. The error bar is the standard error of the mean. The effects range-low (ERL) is the 

concentration below which the expected incidence of adverse effects is low (6 percent). The effects range-median

(ERM) is the concentration above which the expected incidence of adverse effects is high (70 percent).

A

B

C
32

199419961998200020022004200620082010201220142016

Ag in sediment (mg/kg) 0.0

0.2

0.4

0.6

0.8

1.0

3.0

3.5

4.0

ERM = 3.7 mg/kg

ERL = 1 mg/kg

Regional 

Background =

0.09 mg/kg

2011 2012 2013 2014 2015 2016

Ag in sediment (mg/kg) 0.0

0.2

0.4

0.6

Regional 

Background =

0.09 mg/kg

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Ag in sediment (mg/kg) 0.0

0.2

0.4

0.6

Regional 

Background =

0.09 mg/kg

Figure 8. Silver in sediments, Palo Alto, Calif., 1994–2015. (A) Data represent partial-extractable silver 

(treatment with 0.6 N hydrochloric acid) in milligrams per kilogram (mg/kg). (B) Data for the past 5 years (2011–

2015). (C) The monthly mean of all samples collected from 1994–2015, illustrating the general seasonal variation in 

Ag. Collections are not made in July, August, and November. The error bar is the standard error of the mean. The 

effects range-low (ERL) is the concentration below which the expected incidence of adverse effects is low (3 

percent). The effects range-median (ERM) is the concentration above which the expected incidence of adverse 

effects is high (93 percent).

A

B

C
33

 

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Hg and Se in sediment (mg/kg)

0.0

0.2

0.4

0.6

0.8

1.0

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Hg and Se in sediment (mg/kg)

0.0

0.2

0.4

0.6

0.8

1.0

2011 2012 2013 2014 2015 2016 

Hg and Se in sediment (mg/kg)

0.0

0.2

0.4

0.6

0.8

1.0

Figure 9. Mercury and selenium in sediments, Palo Alto, Calif., 1994–2015. (A) Mercury (); selenium () in 

milligrams per kilogram (mg/kg). (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Se and Hg. Collections are not made in 

July, August, and November. The error bar is the standard error of the mean. 

A

B

C
34

Year

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015

Cu in clam tissue (mg/kg)

0

100

200

300

400

Figure 10. Annual mean copper concentrations in milligrams per kilogram (mg/kg) in the clam Macoma petalum, 

Palo Alto, Calif., 1977–2015. Values are the annual (grand) means for 7 to 12 separate samples per year and error 

bars are standard errors of those means.
35

Year

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015

Ag in clam tissue (mg/kg)

0

50

100

150

Figure 11. Annual mean silver concentrations in milligrams per kilogram (mg/kg) in the clam Macoma petalum, 

Palo Alto, Calif., 1977–2015. Values are the annual (grand) means for 7 to 12 separate samples per year and error 

bars are standard errors of those means.
36

 1994 

1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Cu in clam tissue (mg/kg)

0

20

40

60

80

100

2011 2012 2013 2014 2015 2016 

Cu in clam tissue (mg/kg)

0

20

40

60

80

100

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Condition Index (mg) and Cu (ug/g dry wt) of M. petalum

0

40

80

120

160

200

CI

Cu

Figure 12. Copper concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015. (A) Each value is 

the mean concentration in milligrams per kilogram (mg/kg) for the sample collected on a given date. The error bar 

is the standard error of the mean. (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Cu and the condition index. Collections are 

not made in July, August, and November. The error bar is the standard error of the mean. 

B

C

A

Condition index (mg) andCu (mg/kg dry wt) of M. petalum
37

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Ag in clam tissue (mg/kg)

0

2

4

6

8

10

12

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Ag in clam tissue (mg/kg)

0

2

4

6

8

10

12

2011 2012 2013 2014 2015 2016 

Ag in clam tissue (mg/kg)

0

2

4

6

8

10

12

Figure 13. Silver concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015. (A) Each value is the 

mean concentration in milligrams per kilogram (mg/kg) for the sample collected on a given date. The error bar is 

the standard error of the mean. (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Ag. Collections are not made in July, 

August, and November. The error bar is the standard error of the mean. 

A

B

C
38

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Cr in clam tissue (mg/kg)

0

2

4

6

8

10

12

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Cr in clam tissue (mg/kg)

0

2

4

6

8

10

12

2011 2012 2013 2014 2015 2016 

Cr in clam tissue (mg/kg)

0

2

4

6

8

10

12

Figure 14. Chromium concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015. (A) Each value is 

the mean concentration in milligrams per kilogram (mg/kg) for the sample collected on a given date. The error bar 

is the standard error of the mean. (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Cr. Collections are not made in July, 

August, and November. The error bar is the standard error of the mean.

A

B

C
39

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Ni in clam tissue (mg/kg)

0

2

4

6

8

10

12

14

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Ni in clam tissue (mg/kg)

0

2

4

6

8

10

12

14

2011 2012 2013 2014 2015 2016 

Ni in clam tissue (mg/kg)

0

2

4

6

8

10

12

14

Figure 15. Nickel concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015. (A) Each value is the 

mean concentration in milligrams per kilogram (mg/kg) for the sample collected on a given date. The error bar is 

the standard error of the mean. (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Ni. Collections are not made in July, 

August, and November. The error bar is the standard error of the mean.

A

B

C
40

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Zn in clam tissue (mg/kg)

0

100

200

300

400

500

600

700

800

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Zn in clam tissue (mg/kg)

0

100

200

300

400

500

600

700

800

2011 2012 2013 2014 2015 2016 

Zn in clam tissue (mg/kg)

0

100

200

300

400

500

600

700

800

Figure 16. Zinc concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015. (A) Each value is the 

mean concentration in milligrams per kilogram (mg/kg) for the sample collected on a given date. The error bar is 

the standard error of the mean. (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Zn. Collections are not made in July, 

August, and November. The error bar is the standard error of the mean.

C

B

A
41

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Hg in clam tissue (mg/kg) 0.2

0.4

0.6

0.8

1.0

2011 2012 2013 2014 2015 2016 

Hg in clam tissue (mg/kg) 0.0

0.2

0.4

0.6

0.8

1.0

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Hg in clam tissue (mg/kg) 0.0

0.2

0.4

0.6

0.8

1.0

Figure 17. Mercury concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015. (A) Each value is 

the mean concentration in milligrams per kilogram (mg/kg) for the sample collected on a given date. The error bar 

is the standard error of the mean. (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Hg. Collections are not made in March, 

May, July, August, October, and November. The error bar is the standard error of the mean.

C

A

B
42

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Se in clam tissue (mg/kg)

2

4

6

8

10

2011 2012 2013 2014 2015 2016 

Se in clam tissue (mg/kg)

0

2

4

6

8

10

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Se in clam tissue (mg/kg)

0

2

4

6

8

10

Figure 18. Selenium concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2015. (A) Each value is 

the mean concentration in milligrams per kilogram (mg/kg) for the sample collected on a given date. The error bar 

is the standard error of the mean. (B) Data for the past 5 years (2011–2015). (C) The monthly mean of all samples 

collected from 1994–2015, illustrating the general seasonal variation in Se. Collections are not made in March, 

May, July, August, October, and November. The error bar is the standard error of the mean.

C

B

A
43

1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 

Tissue weight in mg (25mm clam)

0

50

100

150

200

250

300

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Tissue weight in mg (25mm clam)

0

50

100

150

200

250

300

2010 2011 2012 2013 2014 2015 2016 

Tissue weight in mg (25mm clam)

0

50

100

150

200

250

300

Figure 19. Condition index of the clam Macoma petalum, Palo Alto, Calif., 1988–2015. (A) The condition index is 

defined as the weight in milligrams (mg) of the soft tissues for an individual clam having a shell length of 25 

millimeters (mm). (B) Condition index over the past 5 years (2011–2015). (C) The monthly mean of samples 

collected from 1988–2015, illustrating the general seasonal variation in condition index. The error bar is the 

standard error of the mean. Samples were not collected in July, August, and November after 1994, and any 

samples collected in those months prior to 1994 were not included for the purposes of the illustration.

C

B

A
44

Year

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

 Percent PercentNon-reproductive Reproductive

-100

-50

0

50

100

Figure 20. Reproductive activity of the clam Macoma petalum, Palo Alto, Calif., 1974–2015. Values are the 

percent of individuals that were either reproductively inactive (non-reproductive; shown in red) or in various stages 

of reproduction (reproductive; shown in green). The percent of non-reproductive individuals is reported as a 

negative value.
45

Year

2010 2011 2012 2013 2014 2015 2016 

 Percent PercentNon-reproductive Reproductive

-100

-50

0

50

100

Figure 21. Reproductive activity of the clam Macoma petalum, Palo Alto, Calif., 2011–2015. Values are the 

percent of individuals that were either reproductively inactive (non-reproductive; shown in red) or in various stages 

of reproduction (reproductive; shown in green). The percent of non-reproductive individuals is reported as a 

negative value.
46

2011 2012 2013 2014 2015 2016 

Number of Species / 54cm

2

0

10

20

30

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Species / 54cm

2

0

10

20

30

Figure 22. Total number of species present at the Palo Alto site, Calif., 1974–2015. Collections were not made 

between 1991 and 1998. Cm, centimeters.
47

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

500

1000

1500

2000

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

500

1000

1500

2000

Figure 23. Total average number of individuals present at the Palo Alto site, Calif., 1974–2015. Collections were 

not made between 1991 and 1998. Cm, centimeters.
48

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

20

40

60

80

100

120

140

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

20

40

60

80

100

120

140

Figure 24. Monthly average abundance of Macoma petalum, Palo Alto, Calif., 1974–2015. Error bars 

represent standard deviation from three replicate samplings. Collections were not made between 1991 and 

1998. Cm, centimeters.
49

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

10

20

30

40

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

2

4

6

8

10

Figure 25. Monthly average abundance of Mya arenaria, Palo Alto, Calif., 1974–2015. Error bars represent

standard deviation from three replicate samplings. Collections were not made between 1991 and 1998. Cm, 

centimeters.
50

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

500

1000

1500

2000

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

300

600

900

Figure 26. Monthly average abundance of Gemma gemma, Palo Alto, Calif., 1974–2015. Error bars represent 

standard deviation from three replicate samplings. Collections were not made between 1991 and 1998. Cm, 

centimeters.
51

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

250

500

750

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

50

100

150

Figure 27. Monthly average abundance of Ampelisca abdita, Palo Alto, Calif., 1974–2015. Error bars represent 

standard deviation from three replicate samplings. Collections were not made between 1991 and 1998. Cm, 

centimeters.
52

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

150

300

450

600

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

25

50

75

100

Figure 28. Monthly average abundance of Streblospio benedicti, Palo Alto, Calif., 1974–2015. Error bars 

represent standard deviation from three replicate samplings. Collections were not made between 1991 and 1998.

Cm, centimeters.
53

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

20

40

60

80

100

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

10

20

30

40

Figure 29. Monthly average abundance of Grandiderella japonica, Palo Alto, Calif., 1974–2015. Error bars 

represent standard deviation from three replicate samplings. Collections were not made between 1991 and 1998.

Cm, centimeters.
54

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

5

10

15

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

5

10

15

Figure 30. Monthly average abundance of Neanthes succinea, Palo Alto, Calif., 1974–2015. Error bars represent 

standard deviation from three replicate samplings. Collections were not made between 1991 and 1998. Cm, 

centimeters.
55

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

20

40

60

80

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

10

20

30

40

Figure 31. Monthly average abundance of Heteromastus filiformis, Palo Alto, Calif., 1974–2015. Error bars 

represent standard deviation from three replicate samplings. Collections were not made between 1991 and 1998. 

Cm, centimeters.
56

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Number of Individuals / 54cm

2

0

200

400

600

800

2011 2012 2013 2014 2015 2016 

Number of Individuals / 54cm

2

0

200

400

600

800

Figure 32. Monthly average abundance of Nippoleucon hinumensis, Palo Alto, Calif., 1974–2015. Error bars 

represent standard deviation from three replicate samplings. Collections were not made between 1991 and 1998.

Cm, centimeters.
57

Abundance (%)

0

20

40

60

80

100

% Spawners 

% Brooders 

% Oviparous 

% mixed Ag in clam tissue (mg/kg)

0

20

40

60

80

100

120

140

1970 1980 1990 2000 2010

Ag in sediment (mg/kg)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 33. Reproductive mode annual abundance with silver concentrations in the clam Macoma petalum and in 

sediment, Palo Alto, Calif., 1974–2015. Annual abundance data is from August of each year. The reproductive 

mode of the top ten ranked species for each year is shown. Brooder: broods young and release juveniles as fully 

functional “miniature adults”; Oviparous: lays eggs in or on sediment; Spawner: releases gametes into water 

column and juveniles settle out of plankton onto sediment surface after growth in the plankton. %, percent; mg/kg, 

milligrams per kilogram.
58

Cu in clam tissue (mg/kg)

0

100

200

300

400

1970 1980 1990 2000 2010

Cu in sediment (mg/kg)

0

20

40

60

80

100

120

Abundance (%)

0

20

40

60

80

100

% Spawners 

% Brooders 

% Oviparous 

% mixed 

Figure 34. Reproductive mode annual abundance with copper concentrations in the clam Macoma petalum and in 

sediment, Palo Alto, Calif., 1974–2015. Annual abundance data is from August of each year. The reproductive 

mode of the top ten ranked species for each year is shown. Brooder: broods young and release juveniles as fully 

functional “miniature adults”; Oviparous: lays eggs in or on sediment; Spawner: releases gametes into water 

column and juveniles settle out of plankton onto sediment surface after growth in the plankton. %, percent; mg/kg, 

milligrams per kilogram.
59

Abundance (%)

0

20

40

60

80

100

% filter feeders 

% sub-surface feeders 

% surface feeders 

% mixed feeders Ag in clam tissue (mg/kg)

0

20

40

60

80

100

120

140

1970 1980 1990 2000 2010

Ag in sediment (mg/kg)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 35. Feeding mode annual abundance with silver concentrations in the clam Macoma petalum and in 

sediment, Palo Alto, Calif., 1974–2015. Annual abundance data is from August of each year. The feeding mode of 

the top ten ranked species for each year is shown. Filter: filters food particles from water column; Subsurface

Deposit: ingests subsurface sediment and removes food from sediment in gut; Surface Deposit: ingests food 

particles on surface sediment; Mixed: capable of filter feeding and surface deposit feeding. %, percent; mg/kg, 

milligrams per kilogram.
60

Cu in clam tissue (mg/kg)

0

100

200

300

400

Abundance (%)

0

20

40

60

80

100

% filter feeders 

% sub-surface feeders 

% surface feeders 

% mixed feeders 

1970 1980 1990 2000 2010

Cu in sediment (mg/kg)

0

20

40

60

80

100

120

Figure 36. Feeding mode annual abundance with copper concentrations in the clam Macoma petalum and in 

sediment, Palo Alto, Calif., 1974–2015. Annual abundance data is from August of each year. The feeding mode of 

the top ten ranked species for each year is shown. Filter: filters food particles from water column; Subsurface 

Deposit: ingests subsurface sediment and removes food from sediment in gut; Surface Deposit: ingests food 

particles on surface sediment; Mixed: capable of filter feeding and surface deposit feeding. %, percent; mg/kg, 

milligrams per kilogram.
61

Figure 37. Species rank-abundance for the benthic community, Palo Alto, Calif., for 1977, 1989, 2002, and 2015. 
62

Figure 38. Species rank-abundance identified by feeding mode, Palo Alto, Calif., for 1977, 1989, 2002, and 2015. 

The feeding mode for each species at each rank shown. Filter: filter food particles from water column; Subsurface 

Deposit: ingests subsurface sediment and removes food from sediment in gut; Surface Deposit: ingests food

particles on surface sediment; Mixed: capable of filter feeding and surface deposit feeding; Carnivore: predator on 

other fauna.
63

Figure 39. Species rank-abundance data identified by reproductive mode, Palo Alto, Calif., for 1977, 1989, 2002, 

and 2015. Reproductive mode for each species at each rank is shown. Brooder: broods young and release 

juveniles as fully functional “miniature adults”; Oviparous: lays eggs in or on sediment; Spawner: releases gametes 

into water column and juveniles settle out of plankton onto sediment surface after growth in the plankton.
64

Table 1. Concentrations of major and minor inorganic elements, total organic carbon, percent of fine particles in surface sediments, and salinity of water 

pooled on the surface of sediments for samples collected from Palo Alto, Calif., 2015. 

[Units for Al, Fe, total organic carbon (TOC), and silt/clay are percent (%) of dry weight. Silt/clay is operationally determined as ≤100 micrometer grain size. Salinity is 

reported in units of parts per thousand (ppt) for water pooled at the sediment surface during low tide. Elemental concentrations for the monthly samples are reported as 

the mean ±1 standard deviation (std) for replicate subsamples (n=2). Units are milligram per kilogram dry weight. Results for TOC, silt/clay, and salinity are for a single 

(n=1) measurement. Means for monthly samples were summarized and reported as the annual mean ± the standard error of the mean (SEM) (n=6 or 9). All concentrations 

are based on near-total extracts, except for silver (Ag), which is based on partial extraction (see text section in Methods). ND, no data]

Date Hg Ni Se

Silt/Clay 

(%)

Salinity 

(ppt)

1/28/2015 3.7 ± 0.2 0.37 ± 0.00 107 ± 6 28 ± 1 3.9 ± 0.1 0.29 99 ± 1.9 0.32 140 ± 2 1.23 ± 0.03 73 26

2/25/2015 4.0 ± 0.1 0.44 ± 0.01 113 ± 0 31 ± 0 4.3 ± 0.02 0.61 104 ± 1.0 0.38 151 ± 1 1.27 ± 0.00 86 24

3/23/2015 4.3 ± 0.0 0.49 ± 0.01 120 ± 3 35 ± 0 4.4 ± 0.2 ND 111 ± 5.8 ND 161 ± 7 1.41 ± 0.00 95 24

4/8/2015 4.2 ± 0.5 0.37 ± 0.01 112 ± 13 32 ± 2 4.2 ± 0.2 0.34 143 ± 5.4 0.35 143 ± 5 1.42 ± 0.01 84 27

5/6/2015 4.1 ± 0.2 0.40 ± 0.01 108 ± 2 33 ± 0 4.1 ± 0.0 ND 99 ± 0.6 ND 137 ± 1 1.52 ± 0.03 79 26

6/8/2015 5.8 ± 0.0 0.35 144 ± 1 44 ± 0 4.7 ± 0.0 0.33 107 ± 0.4 0.37 157 ± 0 1.58 ± 0.01 73 30

9/29/2015 5.2 ± 0.3 0.10 ± 0.00 130 ± 7 42 ± 2 4.1 ± 0.2 0.39 96 ± 3.8 0.44 142 ± 5 1.22 ± 0.01 79 30

10/28/2015 4.3 ± 0.0 0.16 ± 0.00 112 ± 4 31 ± 0 3.7 ± 0.0 ND 85 ± 0.2 ND 114 ± 0 0.91 ± 0.14 68 29

12/21/2015 4.4 ± 0.2 0.26 ± 0.00 116 ± 8 33 ± 2 3.8 ± 0.2 0.67 77 ± 3.2 0.30 109 ± 6 0.98 ± 0.01 66 23

Annual Mean: 0.44 0.36 78 27

SEM: 0.07 0.02 3 1

Zn TOC (%)

4.4 0.33 118 34 4.1 102 139 1.28

Al (%) Ag Cr Cu Fe (%)

0.2 0.04 4 2 0.1 6 6 0.08
65

Table 2. Concentrations of trace metals in and the condition index for the clam Macoma petalum, Palo Alto, Calif., 2015. 

[Monthly data are the mean and standard deviation for replicate composites (n=11–13, n=3 for Se and Hg). Means for monthly samples were summarized and reported as 

the annual mean ± the standard error (SEM) (n=6 or 9). All concentrations are based on near-total extracts. Elemental concentrations are milligram per kilogram soft 

tissue dry weight. The condition index is the soft tissue weight in milligrams of a clam of 25-millimeter shell length. <MDL, less than the method detection limit; ND, no 

data] 

Date

Condition 

Index

1/28/2015 5.5 ± 1.3 4.3 ± 0.8 48 ± 8 0.51 ± 0.08 8.4 ± 1.4 5.07 ± 0.50 242 ± 69 80

2/25/2015 5.9 ± 2.3 5.1 ± 1.3 52 ± 13 0.49 ± 0.14 9.4 ± 1.3 5.00 ± 0.10 348 ± 87 65

3/23/2015 1.9 ± 1.0 2.6 ± 0.5 24 ± 7 ND 5.3 ± 0.5 ND 239 ± 45 145

4/8/2015 1.8 ± 1.3 1.6 ± 0.4 23 ± 7 0.36 ± 0.16 4.1 ± 0.6 4.22 ± 0.61 199 ± 45 183

5/6/2015 1.3 ± 0.8 1.7 ± 1.2 24 ± 14 ND 3.2 ± 1.2 ND 165 ± 33 228

6/8/2015 1.2 ± 0.4 1.7 ± 0.7 23 ± 9 0.24 ± 0.08 3.6 ± 0.9 3.07 ± 0.74 183 ± 47 195

9/29/2015 4.4 ± 2.6 <MDL 75 ± 44 0.55 ± 0.07 5.5 ± 1.4 4.93 ± 0.13 163 ± 43 87

10/25/2015 4.3 ± 3.5 1.9 ± 1.0 68 ± 49 ND 5.8 ± 2.2 ND 128 ± 64 123

12/21/2015 3.2 ± 2.3 1.8 ± 1.1 50 ± 36 0.45 ± 0.24 4.2 ± 2.0 4.63 ± 1.32 93 ± 43 99

Annual Mean: 134

SEM: 0.31 19

Hg Ni

0.43

0.05 25

Ag Cr Cu Zn

195

0.6 0.5 7 0.7

3.3 2.6 43 5.5

Se

4.49
66

Table 3. Reproduction data for Macoma petalum, Palo Alto, Calif., 2015.

[Data are percentage of clams in each stage of reproduction. Reproductive represents the percentage of clams in Active, 

Ripe, and Spawning stages. Non-reproductive represents the percentage of clams in Inactive and Spent stages. Spent means 

the clams have released all their gametes. ND, no data; n, number of clams analyzed] 

Date Inactive Active Ripe Spawning Spent n Reproductive Nonreproductive

28-Jan-15 0.0 0.0 90.0 10.0 0.0 10 100.0 0

26-Feb-15 0.0 0.0 40.0 60.0 0.0 10 100.0 0

23-Mar-15 0.0 0.0 40.0 60.0 0.0 10 100.0 0

8-Apr-15 0.0 0.0 10.0 10.0 80.0 10 20.0 -80

6-May-15 0.0 0.0 0.0 50.0 50.0 10 50.0 -50

8-Jun-15 0.0 0.0 0.0 0.0 100.0 10 0.0 -100

1-Jul-15 ND ND ND ND ND ND ND ND

1-Aug-15 ND ND ND ND ND ND ND ND

29-Sep-15 90.0 10.0 0.0 0.0 0.0 10 10.0 -90

1-Nov-15 ND ND ND ND ND ND ND ND

28-Oct-15 10.0 70.0 20.0 0.0 0.0 10 90.0 -10

21-Dec-15 0.0 0.0 100.0 0.0 0.0 10 100.0 0
67

Appendix 1. Certified concentrations and the percent recoveries of inorganic 

elements in National Institute of Science and Technology Standard Reference 

Material 2709a (San Joaquin Soil) and 2711a (Montana Soil) prepared in 2015. 

[μg/g, micrograms per gram; SRM, standard reference material] 

Constituent

Number 

of 

analyses

Dilution 

ratio

Certified concentration, 

in μg/g

Mean SRM recovery,

in percent

95-percent 

confidence interval 

for SRM recovery, 

in percent

SRM 2709a - Near-total metal extraction

Aluminum 11 1:10 73,700 49 46 – 51

Chromium 11 1:10 130 68 64 – 71

Copper 10 1:10 33.9 76 73 – 80

Iron 11 1:10 33,600 86 83 – 88

Lead 11 1:10 17.3 56 51 – 61

Manganese 11 1:10 529 85 82 – 88

Nickel 11 1:10 85 87 86 – 89

Silver unknown

Vanadium 11 1:10 110 89 83 – 95

Zinc 11 1:10 103 94 91 – 96

SRM 2711a - Near-total metal extraction

Aluminum 17 1:10 67,200 40 38 – 42

Chromium 17 1:10 52.3 58 54 – 62

Copper 17 1:10 140 89 87 – 92

Iron 17 1:10 28,200 81 79 – 83

Lead 17 1:10 1,410 95 93 – 97

Manganese 17 1:10 675 77 74 – 79

Nickel 17 1:10 21.7 88 86 – 90

Silver 17 1:1 6 90 88 – 93

Vanadium 17 1:10 81 87 81 – 93

Zinc 17 1:10 414 98 95 – 101
68

Appendix 2. Certified concentrations and the percent recoveries of inorganic 

elements in National Institute of Science and Technology Standard Reference 

Material 2976 (Mussel Tissue) and 1566b (Oyster Tissue) prepared in 2015. 

[Samples were not diluted prior to analysis; μg/g, micrograms per gram; SRM, standard reference material]

Constituent Number of 

analyses

Certified concentration, 

in μg/g

Mean SRM recovery, in 

percent

95-percent confidence 

interval for SRM recovery, in 

percent

SRM 2976

Cadmium 18 0.82 127 126 – 128

Chromium 18 0.5 109 105 – 113

Copper 18 4.02 90.7 89.7 – 91.6

Lead 18 1.19 77.1 76.0 – 78.2

Nickel 18 0.93 68.9 68.2 – 69.7

Silver 18 0.011 <MRL

Vanadium NA unknown unknown unknown

Zinc 18 137 95.7 94.6 96.9

SRM 1566b

Cadmium 15 2.48 87 71 – 102

Chromium NA unknown unknown unknown

Copper 15 71.6 84 71.9 – 95.3

Lead 15 0.308 95 79 – 111

Nickel 15 1.04 76 62.7 – 89.9

Silver 2 0.666 92 91.5 – 93.7

Vanadium 15 0.577 84 72.4 – 96.3

Zinc 15 1,424 43 31.4 – 53.7

SRM Tort2

Cadmium 6 26.7 97 94 – 100

Chromium NA unknown

Copper 6 106 87 82 – 91

Lead 6 0.35 104 93 – 115

Nickel 6 2.5 77 70 – 83

Silver 6 unknown

Vanadium 6 1.64 66 46 – 87

Zinc 6 180 98 92 – 103
69

Appendix 3. Mercury and selenium concentrations determined in sample splits 

of surface sediments and Macoma petalum collected at Palo Alto, Calif., 2015. 

[One sediment sample and one clam tissue sample were split and analyzed for Se and Hg. The split results are shown here. 

Units are milligrams per kilogram dry weight] 

Date Sample ID Sediment M. petalum

Mercury Selenium Mercury Selenium

Jan. 2015 R3 0.42

R3- duplicate 0.44

June 2015 R1 0.33

R1- duplicate 0.33

Appendix 4. Certified and measured concentrations of mercury and selenium in 

standard reference materials analyzed in 2015. 

[Concentration is reported as milligram per kilogram. SRM, standard reference material] 

Mercury Selenium

SRM Observed Certified Percent 

recovery

Observed Certified Percent 

recovery

PACS-3 2.83 ± 0.01 3.04 ± 0.2 94 1.03

NIST-2976 0.059 ± 

0.002 0.061 ± 0.004 98 1.81 1.80 ± 0.15 100

TORT-3 0.27 ± 0.03 0.292 ± 0.022 93 10.5 10.9 ± 1.0 96
70

Appendix 5. Method detection limits and reporting levels for inductively coupled plasma-optical emission 

spectrophotometry methods.

[Concentration is reported as milligrams per liter; MDL, method detection limit; MRL, method reporting limit] 

Method Marker Ag Al Cd Cr Cu Fe Mn Ni Pb V Zn

Sediment MDL 0.0003 0.0255 0.0001 0.0100 0.0024 0.0327 0.0034 0.0005 0.0026 0.0005 0.0072

MRL 0.0006 0.0509 0.0002 0.0199 0.0048 0.0654 0.0067 0.0010 0.0051 0.0010 0.0143

Tissue MDL 0.0007 0.0092 0.0002 0.0120 0.0020 0.0094 0.0010 0.0002 0.0030 0.0002 0.0022

MRL 0.0013 0.0184 0.0003 0.0240 0.0039 0.0189 0.0020 0.0005 0.0059 0.0004 0.0043 
71

Appendix 6. Statistical summary of percentage of sediment in samples composed of clay- and silt-sized 

particles, collected from Palo Alto, Calif., 1994–2015. 

[Statistical results are for percent fine-grained particles (silt and clay, ≤100 micrometer) observed each month for N collections made during the period 1994–2015. Data 

for percent fines for 2004, which contain unquantifiable biases due to errors in sample processing, are not included in these statistical calculations]

Month N Maximum Minimum Mean Median

January 20 96 46 76 76

February 20 98 32 83 87

March 20 98 24 80 85

April 20 96 50 84 86

May 15 95 35 77 80

June 20 95 46 73 71

July 1 69 69 69 69

August 1 48 48 48 48

September 20 84 25 59 60

October 16 84 39 64 65

November 3 66 50 59 61

December 20 95 48 74 74
72

Appendix 7. Statistical summary of silver and copper concentrations in sediment and the clam Macoma 

petalum, Palo Alto, Calif., for 2015 and 1977–2015. 

[The 2015 column presents the mean and standard error of the monthly samples. Mean, median, minimum, and maximum are calculated from the annual means during 

the period from 1977–2015. Units are milligrams per kilogram dry weight of soft tissue for the clam (Macoma petalum) and milligram per kilogram dry weight for 

sediment] 

Sample type Element Method 2015 Mean Median Minimum Maximum

Sediment Ag Partial extraction 0.33 ± 0.04 0.50 0.36 0.20 1.62

Cu Partial extraction 13 ± 1 23 19 13 55

Cu Near total 34 ± 2 44 43 30 86

M. petalum Ag Tissue digest 3.3 ± 0.6 23 5 1.8 106

Cu Tissue digest 43 ± 7 77 43 24 287
73

Appendix 8. Complete list of benthic species found at Palo Alto in the year 2015. 

[Three samples are taken at each sampling event. The mean and standard deviation (std dev) of the three samples are shown] 
74

Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev

PHYLUM ANNELIDA

Class Oligochaeta

Naididae unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Oligochaeta unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Tubificidae unid. spp. 0.7 0.6 23.7 31.0 1.7 2.9 4.7 3.8 0.0 0.0 9.0 15.6 12.3 8.1 29.0 14.5 1.0 1.7 63.3 56.8

Class Polychaeta

Capitella capitata complex 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Cirratulidae unid. spp. 0.3 0.6 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.7 0.6 0.0 0.0 0.3 0.6 0.3 0.6

Eteone lighti 4.0 2.0 3.0 1.0 2.0 1.0 5.0 2.6 1.3 1.2 4.7 3.2 3.0 3.6 2.3 2.1 1.3 0.6 2.3 3.2

Eteone unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Euchone limnicola 1.3 1.5 1.0 1.0 1.0 1.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Euchone unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Glycera unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Glycinde armigera 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Glycinde picta 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Glycinde unid. sp. SF1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Glycinde unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Harmothoe imbricata 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Heteromastus filiformis 2.3 2.5 3.0 3.0 0.3 0.6 0.3 0.6 0.3 0.6 2.7 2.1 5.0 1.0 8.3 2.1 0.7 0.6 6.3 1.5

Maldanidae unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Marphysa sanguinea 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Neanthes succinea 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Polychaeta unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Polydora cornuta 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6

Polydora unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Pseudopolydora kempi 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Pseudopolydora paucibranchiata 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Sabaco elongatus 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Sphaerosyllis californiensis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Sphaerosyllis erinaceus 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Sphaerosyllis unid. sp. A 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Streblospio benedicti 11.7 14.6 0.0 0.0 1.0 1.7 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 6.3 6.7 0.0 0.0 0.0 0.0

Spionidae unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

5/19/2015

TAXON

1/23/2015 2/23/2015 3/24/2015 4/22/2015 6/18/2015 8/14/2015 9/29/2015 10/28/2015 11/23/2015
75

Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev

PHYLUM ARTHROPODA

Class Arachnida

Acari 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Class Copepoda

Calanoida unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Harpacticoida unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Class Insecta

Chironomidae unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Class Malacostraca

Americhelidium unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Ampelisca abdita 83.0 7.8 69.3 18.5 87.0 17.1 168.7 31.5 129.7 21.4 157.3 23.4 43.3 5.9 50.7 27.0 41.0 15.9 29.3 8.4

Ampithoe unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Callianassidae unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Caprella californica 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Corophium alienense 2.3 0.6 4.0 1.7 33.0 31.7 6.3 5.5 6.7 3.8 5.7 0.6 27.7 2.1 38.3 37.6 23.0 4.4 52.7 29.1

Corophium heteroceratum 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Corophium spinicorne 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Corophium unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Corophiidae unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Crangon nigricauda 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0

Cumella vulgaris 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Eochelidium cf. miraculum 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Eogammarus confervicolus 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Gnorisphaeroma oregonensis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Grandidierella japonica 6.7 0.6 4.3 1.5 20.3 5.5 3.3 2.1 0.7 0.6 11.0 0.0 0.0 0.0 21.7 14.6 17.7 9.8 6.0 1.7

Hemigrapsus oregonensis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Melita nitida 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Melita unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Monocorophium acherusicum 1.3 1.2 0.7 0.6 3.7 3.5 0.0 0.0 0.7 1.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Monocorophium insidiosum 0.3 0.6 3.0 1.7 5.0 3.6 2.0 2.0 1.3 1.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Monocorophium unid. spp. 2.3 2.5 2.0 1.0 8.3 4.9 2.0 2.6 1.3 0.6 1.3 1.5 0.0 0.0 45.0 26.1 0.0 0.0 0.0 0.0

Mysidacea unid. spp. 0.7 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Nippoleucon hinumensis 15.7 6.7 6.0 2.6 17.0 11.5 77.3 23.1 108.3 10.2 187.0 42.2 71.7 37.2 44.7 22.2 5.3 8.4 0.0 0.0

Sinelobus unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.3 0.6 0.0 0.0 0.0 0.0

Sphaeromatidae unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Synidotea laevidorsalis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Synidotea unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Class Ostacoda

Eusarsiella zostericola 33.3 7.6 34.3 3.8 22.3 6.7 8.3 5.1 7.0 3.0 7.3 3.2 14.7 4.0 0.0 0.0 0.0 0.0 0.0 0.0

Cyprideis unid. spp. 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Class Thecostraca

Amphibalanus improvisus 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Balanomorpha unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Cirripedia unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

TAXON

1/23/2015 2/23/2015 3/24/2015 4/22/2015 5/19/2015 6/18/2015 8/14/2015 9/29/2015 10/28/2015 11/23/2015
76

Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev Mean std dev

PHYLUM CNIDARIA

Class Anthozoa

Actiniaria - attached 1.7 0.6 2.0 2.0 0.0 0.0 0.7 0.6 0.0 0.0 0.0 0.0 0.3 0.6 1.7 1.5 4.3 3.5 6.3 6.7

Actiniaria - burrowing 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Actiniaria unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

PHYLUM MOLLUSCA

Class Bivalvia

Bivalvia unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Gemma gemma 291.0 59.6 457.0 15.4 431.0 89.6 349.3 74.4 521.3 270.6 166.7 107.8 188.3 36.3 298.7 133.8 233.7 282.2 76.0 14.0

Macoma petalum 1.0 1.0 3.0 1.0 1.3 0.6 3.0 1.7 3.7 2.1 2.7 1.2 2.0 1.0 2.3 1.5 1.7 1.5 2.3 0.6

Macoma unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Musculista senhousia 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Mya arenaria 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 0.3 0.6 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Potamocorbula amurensis 1.0 1.0 1.3 0.6 0.7 0.6 0.0 0.0 0.0 0.0 1.3 1.2 0.3 0.6 0.3 0.6 0.3 0.6 0.0 0.0

Rochefortia grippi 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Rochefortia unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Tellinidae unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Class Gastropoda

Gastropoda unid. sp. B 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Ilyanassa obsoleta 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Odetta bisuturalis 4.3 3.5 3.0 1.7 2.0 3.5 0.3 0.6 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Philine unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0

Pyramidellidae unid. sp. A 0.7 0.6 1.7 1.5 0.7 1.2 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Urosalpinx cinerea 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

PHYLUM NEMATODA

Nematoda unid. spp. 0.3 0.6 0.0 0.0 0.0 0.0 0.7 0.6 0.0 0.0 0.0 0.0 0.7 1.2 0.0 0.0 0.0 0.0 0.0 0.0

PHYLUM PLATYHELMINTHES

Class Turbellaria

Turbellaria unid. sp. A 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Turbellaria unid. spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

9/29/2015 10/28/2015 11/23/2015

TAXON

1/23/2015 2/23/2015 3/24/2015 4/22/2015 5/19/2015 6/18/2015 8/14/2015
77

Appendix 9. Benthic species name changes as of 2015. 

Current species name: Formerly documented as

PHYLUM ANNELIDA

Class Oligochaeta

Naididae unid. spp. Naididae

Oligochaeta unid. spp. Oligochaeta, Unid. Oligochaeta family

Tubificidae unid. spp. Tubificidae

Class Polychaeta

Capitella capitata complex Capitella "capitata"

Cirratulidae unid. spp. Tharyx spp. ?, Cirratulidae

Eteone unid. spp. Eteone spp., Eteone ?californica

Euchone unid. spp. Euchone spp.

Glycera unid. spp. Glycera spp.

Glycinde picta Glycinde polygnatha

Glycinde unid. sp. SF1 Glycinde sp. SF1

Glycinde unid. spp. Glycinde spp.

Maldanidae unid. spp. Unid. Malanidae

Polychaeta unid. spp. Unid. Polychaeta, Polychaeta

Polydora cornuta Polydora lighti, Polydora ligni

Polydora unid. spp. Polydora spp.

Sphaerosyllis unid. sp. A Sphaerosyllis spp.

Spionidae unid. spp. Unid. Spionidae, Spionidae Unidentified

PHYLUM ARTHROPODA

Class Copepoda

Calanoida unid. spp. Calinoida

Harpacticoida unid. spp. Harpacticoida

Class Insecta

Chironomidae unid. spp. Chironomidae

Class Malacostraca

Americhelidium unid. spp. Americhelidium spp., Synchelidium spp.

Ampithoe unid. spp. Ampithoe spp.

Callianassidae unid. spp. Callianassidae, Callianassidae unidentified

Corophium unid. spp. Corophiidae - unidentified

Corophiidae unid. spp. Corophium spp.

Eogammarus confervicolus Anisogammarus confervicolus

Gnorisphaeroma oregonensis Gnorisphaeroma oregonensis, Gnorimosphaeroma oregonensis

Melita unid. spp. Melita spp.

Monocorophium acherusicum Corophium acherusicum

Monocorophium insidiosum Corophium insidiosum
78

Current species name: Formerly documented as 

Monocorophium unid. spp. Corophium ?insidiosum, Corophium spp. (female and juvenile), 

Corophium spp. (male), Monocorophium spp.

Mysidacea unid. spp. Mysidacea

Nippoleucon hinumensis Hemileucon hinumensis

Sinelobus unid. spp. Sinelobus stanfordi, Sinolobus spp., Sinolobus stanfordi, Tanais 

spp.

Sphaeromatidae unid. spp. Sphaeromatidae (juv.), Sphaeromatidae unid., Dynamella spp.

Synidotea unid. spp. Synidotea spp.

Class Ostacoda

Eusarsiella zostericola Sarsiella zostericola

Cyprideis unid. spp. Cyprideis spp.

Class Thecostraca

Amphibalanus improvisus Balanus improvises

Balanomorpha unid. spp. Balanus ?aquila, Balanus spp., Unid. Balanomorpha, Balanomorpha 

– unidentified

Cirripedia unid. spp. Cirripedia

PHYLUM CNIDARIA

Class Anthozoa

Actiniaria unid. spp. Anthozoa, Unid. Actiniaria

PHYLUM MOLLUSCA

Class Bivalvia

Bivalvia unid. spp. Unid. Bivalvia

Macoma petalum Macoma balthica

Macoma unid. spp. Macoma spp.

Potamocorbula amurensis Corbula amurensis

Rochefortia unid. spp. Rochefortia spp.

Tellinidae unid. spp. Tellinidae

Class Gastropoda

Gastropoda unid. sp. B Unidentified Gastropoda B

Ilyanassa obsoleta Nassarius obsoletus

Odetta bisuturalis Boonea bisuturalis, Odostomia fetella

Philine unid. spp. Philine spp.

Pyramidellidae unid. sp. A Odostomia spp., Pyramidellidae, Unidentified Gastropod A

PHYLUM NEMATODA

Nematoda unid. spp. Nematoda

PHYLUM PLATYHELMINTHES

Class Turbellaria

Turbellaria unid. sp. A Planariidae A

Turbellaria unid. spp. Turbellaria