U.S. Department of the Interior

U.S. Geological Survey

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—2017

By Daniel J. Cain, Janet K. Thompson, Francis Parchaso, Sarah Pearson, Robin Stewart, Mathew Turner, David 

Barasch, Ané Slabic, and Samuel N. Luoma 

Open-File Report 2018–1107
U.S. Department of the Interior

RYAN K. ZINKE, Secretary 

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2018 

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Suggested citation:

Cain, D.J., Thompson, J.K., Parchaso, F., Pearson, S., Stewart, R., Turner, M., Barasch, D., Slabic, A., and 

Luoma, S.N., 2018, 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—2017: U.S. Geological Survey 

Open-File Report 2018–1107, 71 p., https://doi.org/10.3133/ofr20181107. 

Cover. Mudflat at Sand Point, Baylands Nature Preserve, Palo Alto, Calif. Photograph by Daniel Cain, U.S. 

Geological Survey, 2017. 

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.............................................................................................................. 8

Sediment................................................................................................................................................ 8

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

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

Analytical, Excluding Mercury and Selenium.............................................................................................. 9

Sample Preparation and Analysis for Mercury and Selenium..................................................................... 9

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

Salinity...................................................................................................................................................... 10

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

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

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

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

Community Analysis ............................................................................................................................ 11

Statistical Analysis.................................................................................................................................... 11

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

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

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

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

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

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

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

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

2017 Observations ................................................................................................................................... 19

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

Acknowledgment ......................................................................................................................................... 20

References Cited......................................................................................................................................... 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 2017................................................................................................ 62

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 2017.......................................................................................................... 63

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

Macoma petalum collected at Palo Alto, Calif., 2017. ........................................................................... 63

Appendix 4. The percent recovery of mercury and selenium in standard reference materials..................... 64

Appendix 5. Method detection limits and reporting levels for Inductively Coupled Plasma Optical Emission 

Spectrophotometry methods. ................................................................................................................ 64

Appendix 6. Correlation matrix of percent of fine-grained particles and chemical properties of surficial 

sediment based on monthly means of all samples collected at Palo Alto, Calif., during the period 

1994–2017 ............................................................................................................................................ 65
iv

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

petalum, Palo Alto, Calif., for 2017 and 1977–2017. ............................................................................. 66

Appendix 8. Reproduction data for Macoma petalum, Palo Alto, Calif., 2013–2017.................................... 66

Appendix 9. Complete list of benthic species found at Palo Alto in the year 2017....................................... 68

Appendix 10. Benthic species name changes as of 2017............................................................................ 71

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, Calif. ................................ 26

3. Surface-water salinity at the Palo Alto site, Calif., 1994–2017........................................................ 27

4. Aluminum, iron, and silt/clay in sediments, Palo Alto, Calif., 1994–2017........................................ 28

5. Chromium and nickel in sediments, Palo Alto, Calif., 1994–2017................................................... 29

6. Copper in sediments, Palo Alto, Calif., 1994–2017......................................................................... 30

7. Zinc in sediments, Palo Alto, Calif., 1994–2017.............................................................................. 31

8. Silver in sediments, Palo Alto, Calif., 1994–2017. .......................................................................... 32

9. Mercury and selenium in sediments, Palo Alto, Calif., 1994–2017. ................................................ 33

10. Condition index of the clam Macoma petalum, Palo Alto, Calif., 1988–2017.................................. 34

11. Copper concentrations in the clam Macoma petalum, Palo Alto, Calif., 1977–2017....................... 35

12. Silver concentrations in the clam Macoma petalum, Palo Alto, Calif., 1997–2017.......................... 36

13. Chromium and nickel concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2017. 37

14. Zinc concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2017............................ 38

15. Mercury concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2017...................... 39

16. Selenium concentrations in the clam Macoma petalum, Palo Alto, Calif., 1994–2017.................... 40

17. Reproductive activity of the clam Macoma petalum, Palo Alto, Calif., 1974–2017.......................... 41

18. Reproductive activity of the clam Macoma petalum, Palo Alto, Calif., 2013–2017.......................... 41

19. Total number of species present at the Palo Alto site, Calif., 1974–2017....................................... 42

20. Total average number of individuals present at the Palo Alto site, Calif., 1974–2017 .................... 43

21. Monthly average abundance of Macoma petalum, Palo Alto, Calif., 1974–2017............................ 44

22. Monthly average abundance of Mya arenaria, Palo Alto, Calif., 1974–2017................................... 45

23. Monthly average abundance of Gemma gemma, Palo Alto, Calif., 1974–2017.............................. 46

24. Monthly average abundance of Ampelisca abdita, Palo Alto, Calif., 1974–2017 ............................ 47

25. Monthly average abundance of Streblospio benedicti, Palo Alto, Calif., 1974–2017 ...................... 48

26. Monthly average abundance of Grandiderella japonica, Palo Alto, Calif., 1974–2017.................... 49

27. Monthly average abundance of Atilla succinea, Palo Alto, Calif., 1974–2017................................. 50

28. Monthly average abundance of Heteromastus filiformis, Palo Alto, Calif., 1974–2017 ................... 51

29. Monthly average abundance of Nippoleucon hinumensis, Palo Alto, Calif., 1974–2017................. 52

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

and in sediment, Palo Alto, Calif., 1974–2017 ................................................................................ 53

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

and in sediment, Palo Alto, Calif., 1974–2017 ................................................................................ 54

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

sediment, Palo Alto, Calif., 1974–2017........................................................................................... 55

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

in sediment, Palo Alto, Calif., 1974–2017 ....................................................................................... 56

34. Species rank-abundance for the benthic community, Palo Alto, Calif., for 2016 and 2017............. 57
v

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

2017................................................................................................................................................ 58

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

2002, and 2017. .............................................................................................................................. 59

Tables

1. Concentrations of fine particles in surface sediments and major and minor inorganic elements for

samples collected from Palo Alto, Calif., 2017................................................................................ 60

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

Calif., 2017. .................................................................................................................................... 61
vi 

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Volume

gallon (gal) 3.785 liter (L) 

Mass

ounce, avoirdupois (oz) 28.35 gram (g) 

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as °F = (1.8 × °C) + 32.

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as °C = (°F – 32) / 1.8.

Supplemental Information

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 25 °C).

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

Activities for radioactive constituents in water are given in picocuries per liter (pCi/L).

Results for measurements of stable isotopes of an element (with symbol E) in water, solids, and dissolved constituents commonly are 

expressed as the relative difference in the ratio of the number of the less abundant isotope (i

E) to the number of the more abundant 

isotope of a sample with respect to a measurement standard.

Note to USGS users: Use of hectare (ha) as an alternative name for square hectometer (hm2) is restricted to the measurement of small 

land or water areas. 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.

Abbreviations

mL milliliter

μΏ-cm microohm per cm

μg/g microgram per gram

mg/kg milligram per kilogram

ppm parts per million

μm micrometer

CI condition index

ERL effects range-low

ERM effects range-median

EPA U.S. Environmental Protection Agency

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

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—2017

By Daniel J. Cain, Janet K. Thompson, Francis Parchaso, Sarah Pearson, Robin Stewart, Mathew Turner, David 

Barasch, Ané Slabic, 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 silver (Ag) and copper (Cu) in 

mud-dwelling animals in this area (Luoma and Cloern, 1982), with strong seasonal variability (Luoma

and others, 1985). Additional studies identified the PARWQCP as a point source for silver and copper

and established the clam Macoma petalum as a biological indicator of metal exposure (Thomson and 

others, 1984). The annual mean concentrations of silver and copper in M. petalum were 104 milligrams 

per kilogram (mg/kg) and 282 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

(Hornberger and others, 2000). Related studies supported the theory that elevated silver concentrations 

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

environmental stress during this time. Opportunistic organisms (capable of fast invasion and 

propagation in disturbed environments) 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 silver and copper in both sediments and clams declined significantly during 

the 1980s (for example, as low as 11 mg/kg silver and 35 mg/kg copper in M. petalum by the end of the 

decade) as the PARWQCP implemented more advanced wastewater treatment and source control 

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

reduced copper discharge from the PARWQCP (Hornberger and others, 2000; data for silver loading 

were not available before 1989). Coincident with the decline in copper and silver 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 less 

opportunistic species became more persistent. Other environmental factors that vary seasonally and 
2

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

discharge from the wastewater treatment plant (Hornberger and others, 2000). The temporal coincidence 

between metals discharge from the plant, metal concentrations in sediment and tissues of M. petalum at 

the site, and the observed biological responses suggested that the recession in metal exposure was 

principally responsible for the observed biological recovery. 

Following the significant reductions in the 1980s, concentrations of silver and copper in 

sediments continued to decline, although much more gradually. Silver concentration of sediment 

remains greater than what may be considered the natural regional background (0.09±0.02 mg/kg) 

(Hornberger and others, 1999). This persistent, low level of contamination likely derives from silver 

introduced to the site before the 1990s. The concentrations of silver and copper in M. petalum have 

fluctuated as much as four-fold. Silver concentrations have declined slightly since the 1990s while Cu 

concentrations have remained fairly stable. At least some of the variation in silver and copper 

concentrations of M. petalum appears related to annual growth and reproductive cycles independently of 

exposure. Contemporary metal concentrations in sediments and tissue of M. petalum likely reflect a 

combination of factors, including 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 silver and copper 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 (Hornberger and others, 2000). Overall, the 

reproductive status of the population has improved and stabilized over the more than 25 years (1990 to 

present) of reduced exposure to silver and copper 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 two months of the event, however, 

which indicated 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 longterm 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. 
3

When the trace metal study started in the late 1970s, the site was already heavily contaminated.

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 owing to elevated metals,

particularly over decadal time scales. 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 silver and copper in wastewater effluent during the 

1980s allowed for biological recovery and the establishment of a more diverse and stable infaunal 

community. 

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, Calif. This report includes the data collected by

U.S. Geological Survey (USGS) scientists for the period January 2017 to December 2017. These append 

to long-term datasets extending back to 1974. A major focus of the report is an integrated description of 

the 2017 data within the context of the longer, multi-decadal dataset. This dataset supports the City of 

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

Significant reductions in silver and copper concentrations in sediment and M. petalum occurred

at the site in the 1980s following the implementation by PARWQCP of advanced wastewater treatment 

and source control measures. Since the 1990s, concentrations of these elements appear to have stabilized 

at concentrations somewhat above silver (Ag) or near copper (Cu) regional background concentrations. 

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 2017, 

concentrations of silver and copper in M. petalum varied seasonally in response to a combination of sitespecific 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. This record suggests that legacy contamination and regional-scale factors now 

largely control sedimentary and bioavailable concentrations of silver and copper, as well as other 

elements of regulatory interest, at the Palo Alto site. 

Analyses of the benthic community structure of a mudflat in south San Francisco Bay 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 (2017), 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 shortlived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 

2017. 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 a concurrent increase in dominance and, in the last several years before 2008, showed 
4

a stable population. H. filiformis abundance increased slightly in 2011–2012 and returned to pre-2011 

numbers in 2017. 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 anoxia. The reproductive mode of most species that 

were present in 2017 is reflective of species that were available either as pelagic larvae or as mobile 

adults. Although oviparous 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 2017 benthic community data, which showed 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, the potential for adverse biological effects, and the response to regulatory 

or management actions (Suter, 2001). 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 repartitioning them from solution to a

solid phase. As a result, sediments may accumulate and retain metals released to an aquatic 

environment. Sediment cores provide a historical record of metal inputs that can reveal anthropogenic 

influences (Förstner and Wittmann, 1979). Specifically, studies of sediment cores in San Francisco Bay 

chronicled metal inputs and suggested that legacy contamination can remain a chronic source of metals 

to the system owing to sediment mixing and redistribution (Hornberger and others, 1999; Van Geen and 

Luoma, 1999). 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, physical and 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 (Phillips and Rainbow, 1993). 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 cause 

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 
5

in diversity and 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 

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

concentration as well as duration. Even at fairly 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. Data from such studies support surveillance and compliance of 

water-quality objectives. 

Permits issued by the California Regional Water Quality Control Board (RWQCB) under the 

National Pollutant Discharge Elimination System (NPDES) to the Palo Alto Regional Water Quality 

Control Plant (PARWQCP) (fig. 1), requires a prescribed self-monitoring program. In addition, the City 

of Palo Alto augments its own monitoring program with data collected by the U.S. Geological Survey 

(USGS). The USGS 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 2017 are presented within the context of more than 40 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 (based on taxonomic analyses). These data 

and those reported earlier (for example, Luoma and others, 1991, 1995a, 1996; Hornberger and others, 

2000; Thompson and others, 2002; Shouse and others, 2003, 2004; Moon and others, 2005; Cain and 

others, 2006; Dyke and others, 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 management issues or programs,

such as total maximum daily loading (TMDL) targets.

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, 2000) and in benthic community structure (Kennish, 1998). This study, with its 

basis in historical data, provides a rare multi-decadal 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 
6

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

by physical 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 interannual 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 represented as

the total soft-tissue weight of a clam standardized to shell length, and is indicative of the physiological 

condition of the animal (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. Hornberger and others (2000) showed that reproductive 

activity of M. petalum 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 silver (Luoma and others, 1995b) and that 

some crustacean and polychaete species are particularly sensitive to elevated sedimentary copper (Rygg, 

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

structure—that is, shifts in the species composition of the macroinvertebrate community that typically 

result in a change in the function of that 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 impose limitations on species as a 

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

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

mode or those species that lay their eggs in the sediment.

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). Therefore, 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 
7

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).

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 copper, silver, and zinc 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 silver and copper, have declined substantially since the original studies as more efficient 

treatment processes and source controls were employed (Hornberger and others, 2000). Frequent 

sampling each year was necessary to characterize those trends because there was significant seasonal 

variability (Luoma and others, 1985; Cain and Luoma, 1990). This report characterizes data for the year 

2017, 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 or life-cycle 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 monthly to 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. Usually, 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 (2017).

During the period 1977–1980, the sampling frequency and composition of M. petalum samples 

differed from the current design. Specifically, samples were collected more frequently to meet different 

study objectives and individual clams were analyzed instead of the current practice of compositing 

clams of similar size (see below). To harmonize the earlier and later datasets, monthly means for the 

1977–1980 period were recalculated as follows. Where more than one sample was collected within a 

single month of a given year, the mean of those samples was calculated. Monthly data for a given year 

were averaged, producing a grand annual mean with the associated standard error of the mean. This 

recalculation of the data changed the 1977–1980 annual means for Ag and Cu slightly. For example, the 

annual concentration of Ag in M. petalum in 1980 was previously reported as 105 mg/kg (Cain and 

others, 2017). The recalculated concentration is 104 mg/kg.
8

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 been described in detail, previously (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.” 

The percentage 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 to 0.6 grams (g). These 

were redried (70 °C), 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 (EPA) 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.

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±1 °C) for 48 hours 

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

Sample Preparation for Metal Analysis, 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±1 °C).

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 HCl for trace-metal analysis.
9

Analytical, Excluding Mercury and Selenium

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 3 composites, each containing a minimum of ~1.25 g wet weight. To meet this 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 °C). The 

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

homogenized the samples were refrozen (-80 °C) and then freeze-dried.

Sediment samples for mercury and selenium analyses were prepared with the same methods 

used for other trace elements (described above and in previous reports, for example Dyke and others 

[2014]).

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 EPA 

Method 1631, Revision E (2002), and for selenium by acid digestion, hydrogen peroxide oxidation, 

hydride generation inductively coupled plasma mass spectrometry (HG-ICP-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 sequential immersion in 

a detergent bath for at least 24 hours, a rinse in deionized water, then immersion in a 10-percent HCl

wash for at least 24 hours, followed by a 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 selenium and mercury) 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. Recoveries of Ag, Cu, Ni, and Zn 

from NIST 2709a and 2711a by the near-total extraction method were generally consistent with those 

reported by NIST for EPA methods 200.7 and 3050B, whereas the near-total extraction method 

recovered a greater percentage of total Al, Cr, and Fe. Recoveries of elements in biological SRMs were 

consistently greater than 80 percent.
10

Analytical precision of mercury and selenium methods were determined in sample splits 

(appendix 3). Coefficients of determination ranged from 0.1 to 2.3 percent.

A variety of standard reference materials were prepared according to the method used for the 

determination of selenium and mercury. Observed concentrations fell within the range of certified 

values for these materials (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 

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 3 parts per thousand 

(‰).

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 (grams) for a clam 

of a particular shell length (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 (Cain and Luoma, 1990). 

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 (Parchaso, 1993). 
11

Community Analysis

Samples for benthic community analysis were collected with a 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 and retained 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, and individuals for each 

species were enumerated. However, some groups, such as the oligochaetes, are still not well defined in 

the Bay, and hence were not enumerated to the species level. Taxonomic work was performed in 

conjunction with a private contractor familiar with the taxonomy of San Francisco Bay invertebrates 

(Susan McCormick, Colfax, Calif.). McCormick also compared and verified her identifications with 

previously identified samples.

Statistical Analysis

Data collected during 2017 are reported as monthly means with associated standard deviations 

(STD) and annual (grand) means of monthly means with associated standard error mean (SEM). 

Correlations are reported as the Pearson product-moment coefficient unless otherwise stated. Groups 

(such as annual metal concentrations) were tested with ANOVA and Kruskal-Wallis. Transformations 

of data for statistical analysis are explained in the results. Differences with a Type I error rate α≤0.05 

were considered significant. Statistical analyses were performed with Statistica v. 13 (Statsoft).

Throughout the report, metals data are illustrated to represent inter-annual variation for the period 1994–

2017 and intra-annual variation over the past 5 years. The general pattern of seasonal variation was 

based on monthly means of all samples collected over the period of record (typically 1994–2017).

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 that has been 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 2017 was 26.5 inches.

(http://cdec.water.ca.gov/) (fig. 2). Salinity varied between 5 and 23‰ during 2017 (fig. 3).

Sediments

Surficial sediment collected in this study is dominated by silt- and clay-sized particles <100 μm, 

typically constituting 50–90 percent of the sampled sediment on a weight basis. These fine sediments 

provide large surface areas for metal sorption. Metal concentrations vary as a function of the ratio of 

surface area to volume of a particle and thus tend to track the percentage of fine particles. The 

percentage of fine particles displays an annual periodicity as do aluminum and iron concentrations (fig. 

4C), and other metals considered in this study (not illustrated). Indeed, for all metals considered in this 

study, other than Hg and total organic carbon (TOC), correlations with the percentage of fines were 

highly significant (r ≥0.87, appendix 6). Thomson-Becker and Luoma (1985) suggested that this intraannual variation in metal concentration is related to changes in the size distribution of sediment particles 

caused by allochthonous inputs and deposition of fine-grained particles in the winter and their 

subsequent wind-driven resuspension in the summer and fall.
12

Chromium and nickel are highly enriched in some geologic formations within the watershed. For

example, in north San Francisco Bay, studies of sediment cores 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, annual concentrations of chromium in 

surface sediment varied between 105 and 163 mg/kg and nickel concentrations varied between 72 and 

100 mg/kg (fig. 5). In 2017, concentrations were 120±12 and 92±9 mg/kg for chromium and nickel, 

respectively (table 1). As with other metals, chromium and nickel concentrations varied seasonally

which may reflect seasonal changes in the particle size distribution of sediments described above and 

inputs from the surrounding watershed.

Concentrations of copper and zinc in sediments are shown with a sediment quality guideline set 

by the National Oceanic and Atmospheric Administration (Long and others, 1995) in figures 6 and 7. 

Long and others (1995) defined the ERL (effects range-low) as the concentration below which the 

incidence of adverse effects on sensitive species is low (<10 percent). The ERLs for copper and for zinc 

are 34 mg/kg and 150 mg/kg, respectively. For most of the record, copper concentration has exceeded 

the ERL on an annual basis (fig. 6). In 2017, the average annual copper concentration was 30±1 (SEM) 

mg/kg (fig. 6, table 1). The partial extractions represent approximately 42 percent of the copper 

recovered in the near-total digest. Over the period 1990 to 2017, copper concentrations have gradually 

declined (p<0.05). Near-total and partially extractable zinc concentrations were below the zinc ERL 

(150 mg/kg) for the entire record (fig. 7, table 1) on an annual basis. Exceedances of near-total zinc 

within some years typically occurred during the winter season (for example, 2015). In 2017, the average 

annual zinc concentration was 112±4 mg/kg with a maximum concentration of 124 mg/kg in April and 

127 mg/kg in December. 

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. During the 1980s, 

concentrations fell dramatically, but since then they have been fairly stable. In 2017, silver 

concentrations averaged 0.21±0.01 mg/kg. During 2017, concentration maxima were observed in April 

and October (0.25 mg/kg), and minima occurred in March, June, and September (0.17–0.18 mg/kg) (fig. 

8, table 1).

Mercury and selenium concentrations in sediment from Palo Alto do not exhibit any obvious 

long-term trends (fig. 9). The median mercury concentration of the annual means is 0.29 mg/kg, with 90 

percent of the values falling between 0.24 and 0.33 mg/kg. Concentrations occasionally exceeded 0.40 

mg/kg (in 2004 and 2015). During 2017, Hg averaged 0.29±0.02 mg/kg (fig. 9, table 1) with the 

minimum in June (0.22 mg/kg) and the maximum in December (0.35 mg/kg). On an annual basis, 

sedimentary selenium has varied between 0.30 and 0.79 mg/kg with no sustained temporal trend over 

the period of the record. In 2017, selenium varied seasonally, with higher concentrations in the early 

part of the year (from 0.52 mg/kg in January to 0.52 mg/kg in April) and then receded to 0.36–0.48 

mg/kg in June through December (fig. 9, table 1). For the year, selenium concentrations averaged 

0.46±0.03 mg/kg.

Clam Tissue

Metal concentrations in the soft tissues of M. 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 (Cain and Luoma, 1990). Growth and 

reproductive cycles are reflected in the condition index (CI). Data on the CI fluctuate seasonally and 

annual cycles differ in magnitude (fig. 10A). Condition index values typically increase through winter to 

a maximum in the spring (pre-spawning period) then taper off through summer/fall (figs. 10B, C). The 
13

pattern of seasonal variation of CI in 2017 was typical for the record, although the spring 

growth/reproductive period was markedly weak (fig. 10B). This is reflected in the annual average CI for 

2017 (107±20 mg) (fig. 10A, table 2).

Exposures to copper and silver at Palo Alto are of special interest because of the high tissue 

concentrations observed at this site in the past (figs. 11, 12, appendix 7). During 1977–1990, the ranges 

in annual concentrations of copper and silver were 35–282 mg/kg and 7.7–104 mg/kg, respectively. 

Since 1990, concentrations have been considerably lower (table 2); median concentrations for copper 

and silver are 33 mg/kg and 3.1 mg/kg, respectively. Annual silver concentrations declined slightly over 

this period (r=-0.63, p<0.001); however, they correlated negatively with the CI, suggesting that the 

temporal trend in silver was at least in part a manifestation of the physiological state of the clam. The 

amplitude of the CI from one year to the next can affect inter-annual variation in metal concentrations. 

The increase in copper (fig. 11) and silver (fig. 12) in 2017 coincides with the fairly low CI.

Intra-annual variations in copper and silver 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 (figs. 11B and 12B). These patterns are 

correlated with the growth and reproductive cycles, as discussed above. For example, over the period of 

1994 to 2017, the seasonal variations in copper and the CI varied inversely of one another (r=-0.98, 

p<0.001) and were of similar magnitude, suggesting that variations in tissue weight driven by growth 

and reproduction and tissue copper concentrations—as well as other elements—are coupled (fig. 11C).

As with copper and silver, tissue concentrations of chromium (fig. 13, table 2), nickel (fig. 13, 

table 2), and zinc (fig. 14, table 2) also exhibited annual cycles of variable magnitude throughout the 

record. None of these elements exhibit a clear temporal trend (either decreasing or increasing) in 

concentration. In 2017, the annual average chromium, nickel, and zinc concentrations were 3.19±0.41, 

5.64±0.37, and 346±22 mg/kg, respectively (table 2).

The average mercury concentration in M. petalum in 2017 was 0.57±0.12 mg/kg (fig. 15, table 

2), which was the highest recorded annual concentration in the time series at the site. A long-term trend 

in mercury concentration is not evident, however (fig. 15A). Intra-annual variation of fall/winter 

maxima and spring/summer minima observed in the preceding 3 years was not evident in 2017. Instead, 

mercury concentrations increased over the course of the year, similar to selenium in clams (see below).

Selenium concentrations in M. petalum averaged 4.96±0.14 mg/kg in 2017 (fig. 16, table 2). The 

mean annual concentrations of selenium have been relatively low and stable since 2011. Intra-annual 

variation was less evident in 2017 with concentrations generally increasing over the year with the 

highest concentration observed in December (5.56 mg/kg) (fig. 16B, table 2).

Reproduction of Macoma petalum

As previously reported, reproductive output in M. petalum appeared to be impaired by high 

concentrations of silver in the tissue of this clam during the early part of the record (Hornberger and 

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

the decline in silver during the 1980s reproductive output increased, and it has remained at relatively 

high levels. Unlike the earlier period, a high percentage of the animals were reproductively active at any 

one time, and they did not stay reproductively inactive for longer than a month or two. Moreover, 

normal seasonal cycling of reproduction—beginning in the fall and continuing through the following 

spring—is evident (figs. 17, 18, appendix 8).
14

Benthic Community

Estimates of species diversity and total animal abundance are fundamental 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 of two in 1998, and after

qualitatively trended upward from 1998 through 2007. Diversity has rebounded since the low in 2008 

(fig. 19). Total animal abundance has varied significantly during the sampling period (fig. 20). 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 (for example, see figure 22, which shows the abundance of the bivalve Mya 

arenaria spiking to a value 5–10 times higher than other periods before returning to more average 

abundance values).

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

any consistent trend between years over the 43-year period from 1974 to 2017 (figs. 21–23). 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. For example, 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 2017.

Six species have shown patterns in their abundance since the 1970s. 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. 24) after 1998 and mostly low 

abundances persisted through 2014. In 2015–2016, A. abdita showed an increase in abundance. The 

second species to show an abundance pattern 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. 25). The abundance of the small 

burrowing crustacean Grandiderella japonica, a deposit feeder, became more seasonally consistent after 

2000 (fig. 26), 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. Alitta succinea, 

a burrowing polychaete that feeds on surface deposits and scavenges for detrital food, showed large 

seasonal fluctuations in abundance throughout the study (fig. 27) and, like other species, its abundance 

declined in 2011 and remains in low numbers in 2017. Two species showed an increase in abundance 

within the time series. The first was the polychaete worm Heteromastus filiformis (fig. 28), a

subsurface-deposit-feeding, burrowing 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. 28). 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. 29) following

its introduction into the bay in 1986 (Cohen and Carlton, 1995). A complete list of the benthic species 
15

found at the Palo Alto site in the year 2017 is shown in appendix 9. The benthic species name changes 

(as of 2017) for the species listed in appendix 9 are shown in appendix 10.

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, spanning 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. The rapid growth required for M. petalum to be found after a dieoff would not happen so quickly. 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 over more 

than 30 days. 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 S. benedicti. This trend 

continued into 2017, when brooder species were more than half of the top 10 most abundant species, 

while oviparous and spawner species made up the rest (fig. 30).

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

did not reveal any relations, except with the concentration of silver and copper in the sediment and in 

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

primarily focus on 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 silver and 

copper until 2008 (fig. 28). 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 oviparous 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 planktonic period (2–3 days) before 

settling back to the mud as juvenile worms (Rasmussen, 1956). The short 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 

then 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 given the variability in abundance of H. filiformis over monthly to decadal time 

scales.

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

24) and the worm S. benedicti (fig. 25) 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 silver and copper 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 
16

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 in February 2008 and have subsequently declined (figs. 24 and 25). 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 taxa in diverse communities 

under 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. 30–33). 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 30–33. 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 silver or copper in the 

environment. It is likely that silver, and probably not copper, adversely affected reproduction of all 

animals (Hornberger and others, 2000). If species with pelagic larvae were transported into the area they 

did not survive to dominate the community. Species having oviparous and mixed (species capable of 

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

worth examining in more detail. The gradual increase in abundance of these oviparous and mixed 

reproduction species 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. 30, 31). Although the percentage is volatile, 

the percentage of 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. 32, 33).

High concentrations of either copper or silver 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 sediment-bound 

contaminants. Filter feeding species are usually the dominant group throughout the dataset, and the 

subsurface deposit feeders are the group that shows the largest increase in dominance after the 1970s

when improved wastewater treatment at PARWQCP decreased silver and copper in proximal sediments. 

The multi-decadal trends presented above for abundances of major-species are 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

(Whittaker, 1965). The plot for 2017 (fig. 34) 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 varied and that the 2017 curve is similar to that seen in 

1989. The series of curves shows a community that was, with the rest of the species having similar 

abundancies, heavily dominated by three species in 1977, 1989, and 2017, versus a community with one 

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

2017, the graph shows a smooth downward slope showing a more homogenized decrease in species 
17

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 

(fig. 35) and reproductive mode (fig. 36). The 1977 community was dominated by filter feeding species 

(species that consume particles in the water column), species that have the option of either filter feeding 

or feeding on the sediment surface (mixed feeders), and two species that feed on food particles on the 

sediment surface. In 1989, the species composition had shifted, relative to 1977, 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 (2017) show the community to be similar to that of 1989, 

with the composition still having greater abundance of subsurface and surface deposit feeders, relative 

to 1977. The species that returned following the defaunation event in January/February 2008 have 

maintained this pattern. Thus, it is unlikely that any of the sediment-borne contaminants considered in 

this study 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. 36). 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. It would appear that 

brooding species have a reproductive advantage over other modes, as they occupied the top-ranking 

position since 1977 (fig. 36). 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. Species that spawn 

their gametes into the water column in combination with those that lay eggs in the sediment (oviparous) 

have sometimes ranked highly in terms of their presence. Interestingly, the reproductive mode of most 

species present in 2017 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 updates and extends previous 

findings (for example, Luoma and others, 1991, 1995a, 1996; Hornberger and others, 2000; Thompson 

and others, 2002; Shouse and others, 2003, 2004; Moon and others, 2005; Cain and others, 2006; Dyke 

and others, 2012, 2014) with additional data from January 2017 through December 2017 to create a 

record spanning more than 40 years. This long-term dataset includes sediment chemistry and tissue 

concentrations of metals (1977–2017 for copper and silver, 1994–2017 for other metals), condition 

index (1988–2017), and reproductive activity in M. petalum and population dynamics of benthic 

invertebrate species (1974–2017). The time series encompasses the period when exceptionally high 

concentrations of copper and silver 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 over multiple time scales.
18

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

highly elevated levels of metals, especially silver and copper, 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 

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

from PARWQCP (concurrent loading data for silver 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, 2000).

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 initially high and 

declining, the benthic community was largely dominated by nonindigenous, opportunistic species. This 

dominance was initially attributed to 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 (Hornberger and others, 2000), 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.

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 decades, and these fluctuations have been reflected in changes in phytoplankton 
19

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 and solute cycling. 

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. These findings

reinforce the authors’ confidence that the changes observed in the benthic community are in large part 

due to local factors.

2017 Observations

Throughout 2017, copper and silver concentrations in sediments remained representative of the 

concentrations observed since 1990, following the significant reductions in concentrations during the 

1980s that coincided with reductions in the discharge of these elements from PARWQCP. Since 1990, 

annual mean copper and silver concentrations have fluctuated modestly. Copper concentrations have 

gradually declined over that period, while silver concentrations have not. Like silver, sedimentary 

concentrations of other elements have varied from year to year but shown no sustained temporal trend.

The most recent results (2017) showed an increase in all metals in M. petalum. The increase in 

copper was particularly notable given that it approached concentrations (on an annual basis) that had not 

been observed since the late 1980s. Mercury concentrations in 2017 were the highest on record. The 

increased levels of metals were coupled with a relatively low condition index, which is indicative of the 

physiological state of the clam. An analysis of factors influencing the physiological condition of M. 

petalum is beyond the scope of this study. However, since the 1990s, metal exposure would seem an 

unlikely causative agent given the low and relatively stable concentrations of metals in the sediments. 

Furthermore, inter-annual variation in copper and silver in M. petalum from 1991 to 2006 did not 

correlate with discharge of copper and silver from PARWQCP (Lorenzi and others, 2007), indicating 

that, as with other elements of regulatory interest, including chromium, nickel, and zinc, regional-scale 

factors now largely influence sedimentary and bioavailable concentrations (see, for example, Luoma 

and others, 1998). In addition to the biotic factors discussed in previous sections, 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 within the bay, accelerated 

erosion of salt marsh banks in recent years, and periods of accretion and erosion of sediment on the 

mudflat.

The long-term dataset that we augment with this report demonstrates various adverse effects of 

contaminants on benthic organisms. Decreasing particulate concentrations of trace metals in the local 

environment have benefited resident populations of invertebrates, as evidenced by increased 

reproductive activity in M. petalum that has been sustained through 2017. In early 2008, the benthic 

community declined, with few animals present in February. This decline was likely the result of a 

natural stressor, such as a sedimentation or freshwater event, and 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 did not 

survive at the study site. 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 of metals in sediment and M. petalum. Shifts in species abundance at the study site 

have been interpreted to be a response to decreasing sediment contaminants within two years of 

improved wastewater treatment at PARWQCP. 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 
20

surface, consume the sediment directly to harvest food particles, and spawn and lay eggs in the 

sediment. Hence, the benthic community now has a greater dependence on sediment for food and 

reproduction relative to the late 1970s, consistent with management practices that have improved 

sediment quality. The 2008–2017 data reveal a community that had a short-term physical stressor but 

not one that was subject to trace-metal contamination. In 2017, the species abundance data continues to 

show signs of a community that has recovered and stabilized, and the constancy of functional groups 

reflects the stability of the ecosystem. Thus, the data from the recent record (that is, within the past three 

decades) reflect the improved ecological condition of the Palo Alto site which appears indicative of an 

integrated regional ecological baseline. This “natural experiment” has given USGS scientists an

opportunity to test various hypotheses on the benthic community response to different stressors. Future 

data will further refine the understanding of the response of this benthic community to natural and 

anthropogenic stressors.

Value of Long-Term Monitoring

This study highlights the importance of long-term ecosystem monitoring. Although monitoring 

studies cannot always unambiguously determine the causes of variation in metal concentrations or 

benthic community structure, time-series data may reveal ecological responses that are distinctively 

associated with human activities. Changes and trends in community structure that may be related to 

anthropogenic stressors, as was seen in this study for multiple trace metals, can be established only with 

a concerted and committed sampling effort of sufficient duration and frequency and data interpretation.

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.

Human activities continue to impact San Francisco Bay and its watershed. Factors that may 

influence metals in the near and long term include climate variation, nonpoint-source runoff and efforts 

to mitigate it, reconnection of reclaimed intertidal areas to the bay, cycling of legacy contamination

within the bay, new and redevelopment of the Bay Area landscape, and sea-level rise. Among emerging 

contaminants of concern are nanomaterials, many of which include metal-based products in forms for 

which environmental scientists and regulators have little or no experience. Only recently have 

quantitative descriptions become available of the bioavailability of trace metals from such sources 

(Croteau and others, 2011, 2014). 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

and informing management and regulatory agencies as human activities within the watershed continue.

Acknowledgment

Le Kieu and Mark Marvin-DiPasquale, U.S. Geological Survey, provided the mercury data.

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Simon, T.P., 2002, Biological response signatures: Boca Raton, Florida, CRC Press, 608 p.

Suter, G.W., II, 2001, Applicability of indicator monitoring to ecological risk assessment: Ecological 

Indicators, v. 1, p. 101–112.

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.
24

Van Geen, A., and Luoma, S.N., 1999, The impact of human activities on sediments of San Francisco 

Bay, California: an overview: Marine Chemistry, v. 64, p. 1–6.

Wang, W., and Fisher, N.S., 1999, Delineating metal accumulation pathways for marine invertebrates: 

Science of the Total Environment, v. 237, p. 459–472.

Weesner, F.M., 1960, General zoological microtechniques: Baltimore, Maryland, The Waverly Press, 

Inc., 230 p.

Whittaker, R.H., 1965, Dominance and diversity in land plant communities—Numerical relations of 

species express the importance of competition in community function and evolution: Science, v. 147, 

no. 3655, p. 250–260.
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 in B) is discharged by way of an 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

1994 1996 

1998 

2000 

2002 

2004 

2006 

2008 

2010 

2012 

2014 

2016 

2018 

Monthly precipitation (inches)

0

2

4

6

8

10

12

14

16

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

Precipitation (inches)

0

5

10

15

20

25

monthly total

cumulative 

A.

B

Figure 2. Precipitation recorded at San Francisco WB AP in San Mateo County, Calif. A, Monthly precipitation for 

the period 1994–2017. B, Monthly (dark bar) and cumulative (light bar) precipitation for 2017. The station 

(identification SFF) is operated by the National Weather Service.
27

A.

B.

Jan.

Feb.

Mar.

Apr.

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

2018

Salinity (‰)

0

5

10

15

20

25

30

35

Figure 3. Surface-water salinity in parts per thousand (‰) at the Palo Alto site, Calif., 1994–2017. A, Monthly 

data (dots) for the period 1994–2017. B, The general seasonal variation as the monthly averages (±1 std, n=23).
28

B.

C.

2013 2014 2015 2016 2017 2018

Fine-grain sediment (% <100 m) 

0

20

40

60

80

100

Al and Fe in sediment (%)

1

2

3

4

5

6

7

8

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

Al and Fe in sediment (%)

2

4

6

8

Fine-grain sediment (% < 100 m)

0

20

40

60

80

100

1990 1995 2000 2005 2010 2015 2020

Al and Fe in sediment (%)

3

4

5

6

7

Al

Fe

Figure 4. Aluminum (Al), iron (Fe), and silt/clay in sediments, Palo Alto, Calif., 1994–2017. %, percent, mg/kg, 

milligrams per kilogram; μm, micrometer. A, Annual concentration of aluminum and iron (extracted by near-total 

digest) for the period 1994–2017. Data are reported as percent. Each value is the grand mean for nine samples per 

year with the standard error of those means (SEM). B, Percent aluminum, iron, and fine sediment (≤100 μm) for 

the period 2013–2017. Data represent the mean values. C, The monthly mean of all samples collected from 1994–

2017, illustrating the general seasonal variation in aluminum, iron, and percent fine sediments. Collections are not 

made in July, August, and November. The error bars are the SEM.
29

A.

B.

2013 2014 2015 2016 2017 2018 

Cr and Ni in sediment (mg/kg)

0

50

100

150

200

1990 1995 2000 2005 2010 2015 2020

Cr and Ni in sediment (mg/kg)

60

80

100

120

140

160

180

Cr 

Ni 

Figure 5. Chromium (Cr) and nickel (Ni) in sediments in milligrams per kilogram (mg/kg), Palo Alto, Calif., 1994–

2017. A, Annual concentration of chromium and nickel for the period 1994–2017. Each value is the grand mean for 

nine samples per year with the standard error of those means (SEM). B, Data for the period 2013–2017. Data 

represent the mean value. 
30

Figure 6. Copper (Cu) in sediments, in milligrams per kilogram (mg/kg), Palo Alto, Calif., 1994–2017. A, Annual 

concentration of near-total and partial-extractable copper for the period 1994–2017. Each value is the grand mean 

for nine samples per year with the standard error of those means (SEM). The dashed line is the effects range low 

(ERL), the concentration below which the expected incidence of adverse effects is low (9 percent). B, Data for the 

period 2013–2017. Data represent the mean value. 
31

Figure 7. Zinc (Zn) in sediments, in milligrams per kilogram (mg/kg), Palo Alto, Calif., 1994–2017. A, Annual 

concentration of near-total and partial-extractable zinc for the period 1994–2017. Each value is the grand mean for 

nine samples per year with the standard error of those means (SEM). The dashed line is the effects range low 

(ERL), the concentration below which the expected incidence of adverse effects is low (9 percent). B, Data for the 

period 2013–2017. Data represent the mean values. 
32

Figure 8. Silver (Ag) in sediments, in milligrams per kilogram (mg/kg), Palo Alto, Calif., 1994–2017. A, Annual 

concentration of silver for the period 1994–2017. Each value is the grand mean for nine samples per year with the 

standard error of those means (SEM). Data represent the annual mean with standard error (SEM). Data represent 

partial-extractable silver (treatment with 0.6 N hydrochloric acid). B, Data for the period 2013–2017. Data represent

the mean values. 

A.

B.

2013 2014 2015 2016 2017 2018 

Ag in sediment (mg/kg)

0.0

0.1

0.2

0.3

0.4

0.5

0.6

1995 2000 2005 2010 2015 2020

Ag in sediment (mg/kg)

0.0

0.1

0.2

0.3

0.4

0.5

0.6
33

Figure 9. Mercury (Hg) and selenium (Se) in sediments, in milligrams per kilogram (mg/kg), Palo Alto, Calif., 

1994–2017. A, Annual concentration of mercury and selenium for the period 1977–2017. Each value is the grand 

mean for 7–12 samples per year with the standard error of those means (SEM). B, Data for the period 2013–2017. 

Data represent the mean value.

B.

A.

2013 2014 2015 2016 2017 2018 

H

g

a

n

d

Se in

s

e

dime

nt (mg/kg)

0.0

0.2

0.4

0.6

0.8

1.0

1995 2000 2005 2010 2015 2020

Hg andSe in sediment (mg/kg)

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

Hg 

Se 
34

Figure 10. Condition index of the clam Macoma petalum, Palo Alto, Calif., 1988–2017. A, Annual condition index. 

The condition index is defined as the weight (milligrams) of the soft tissues for an individual clam having a shell 

length of 25 millimeters (mm). Each value is the grand mean for nine samples with the standard error of the mean 

for those samples (SEM). B, Condition index over the period 2013–2017. C, The monthly mean of samples 

collected from 1988–2017, illustrating the general seasonal variation in condition index. The error bar is the SEM. 

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.

A.

B.

C.

Jan. Feb. Mar. Apr. May June July Aug. Sept. Oct. Nov. Dec.

Tissue weight in mg (25m

mclam)

0

100

200

300

400

2013 2014 2015 2016 2017 2018 

Tissue weight in mg (25m

mclam)

0

100

200

300

400

1988

1990

1992

1994

1996

1998

2000

2002

2004

2006

2008

2010

2012

2014

2016

2018

Tissue weight in mg (25m

mclam)

0

50

100

150

200
35

Figure 11. Copper (Cu) concentrations in the clam Macoma petalum in milligrams per kilogram (mg/kg), Palo Alto, 

Calif., 1977–2017. A, Annual concentration for the period 1977–2017. Each value is the grand mean for 7–12 

samples per year with the standard error of those means (SEM). B, Data for the period 2013–2017. Each value 

represents the mean concentration for the sample collected on a given date. The error bar is the SEM. C, The 

monthly mean of all samples collected from 1994–2017, illustrating the general seasonal variation in copper and 

the condition index (CI). Collections are not made in July, August, and November. The error bar is the SEM.

A.

B.

C.

2013 2014 2015 2016 2017 2018 

Cu in clamtissue (mg/kg)

0

50

100

150

200

250

1980 1990 2000 2010 2020 

Cu in clamtissue (mg/kg)

0

50

100

150

200

250

300

350

400

Jan. Feb. Mar. Apr. May June July Aug Sept. Oct. Nov. Dec.

Condition Index (mg)

Cu concentration (mg/kg)

0

20

40

60

80

100

120

140

160

180

200

220

Cu 

CI
36

Figure 12. Silver (Ag) concentrations in the clam Macoma petalum in milligrams per kilogram (mg/kg), Palo Alto, 

Calif., 1997–2017. A, Annual concentration for the period 1977–2017. Each value is the grand mean for 7–12 

samples per year with the standard error of those means (SEM). B, Data for the period 2013–2017. Each value 

represents the mean concentration for the sample collected on a given date. The error bar is the SEM.

A.

B.

2013 2014 2015 2016 2017 2018 

Ag in

cla

mtis

s

u

e (mg/kg)

0

2

4

6

8

10

1980 1990 2000 2010 2020 

Ag in

cla

mtis

s

u

e (mg/kg)

0

20

40

60

80

100

120

140
37

Figure 13. Chromium (Cr) and nickel (Ni) concentrations, in milligrams per kilogram (mg/kg), in the clam Macoma 

petalum, Palo Alto, Calif., 1994–2017. A, Annual concentration of chromium and nickel for the period 1994–2017. 

Each value is the grand mean concentration for 7–12 samples per year with the standard error of those means 

(SEM). B, Data for the period 2013–2017. Each value represents the mean concentration for the sample collected 

on a given date. The error bar is the SEM.

A.

B.

2013 2014 2015 2016 2017 2018 

Cr a

n

d

Ni in

cla

mtis

s

u

e (mg/kg)

0

2

4

6

8

10

12

1994

1996

1998

2000

2002

2004

2006

2008

2010

2012

2014

2016

2018

Cr a

n

d

Ni in

cla

mtis

s

u

e (mg/kg)

0

2

4

6

8

10

12

Cr 

Ni 
38

A.

B.

2013 2014 2015 2016 2017 2018 

Zn in clam tissue (mg/kg)

0

100

200

300

400

500

600

1994 1996 

1998 

2000 

2002 

2004 

2006 

2008 

2010 

2012 

2014 

2016 

2018 

Zn in clam tissue (mg/kg)

0

100

200

300

400

500

600

Figure 14. Zinc (Zn) concentrations, in milligrams per kilogram (mg/kg), in the clam Macoma petalum, Palo Alto, 

Calif., 1994–2017. A, Annual concentration of zinc. Each value is the grand mean concentration for 7–12 samples 

per year with the standard error of those means (SEM). B, Data for the period 2013–2017. Each value represents

the mean concentration for the sample collected on a given date. The error bar is the SEM.
39

A.

B.

2013 2014 2015 2016 2017 2018 

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 2018 

Hg in clam tissue (mg/kg)

0.0

0.2

0.4

0.6

0.8

1.0

Figure 15. Mercury (Hg) concentrations, in milligrams per kilogram (mg/kg), in the clam Macoma petalum, Palo 

Alto, Calif., 1994–2017. A, Annual concentration of mercury. Each value is the grand mean concentration for six

samples per year with the standard error of those means (SEM). B, Data for the period 2013–2017. Each value 

represents the mean concentration for the sample collected on a given date. The error bar is the SEM.
40

A.

B.

2013 2014 2015 2016 2017 2018 

Se in clam tissue (mg/kg)

0

2

4

6

8

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 

Se in clam tissue (mg/kg)

0

2

4

6

8

Figure 16. Selenium (Se) concentrations, in milligrams per kilogram (mg/kg), in the clam Macoma petalum, Palo 

Alto, Calif., 1994–2017. A, Annual concentration of selenium. Each value is the grand mean concentration for 6 

samples per year with the standard error of those means (SEM). B, Data for the period 2013–2017. Each value 

represents the mean concentration for the sample collected on a given date. The error bar is the SEM.
41

Year

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

 Percent Percent

Non-reproductive Reproductive

-100

-50

0

50

100

Figure 17. Reproductive activity of the clam Macoma petalum, Palo Alto, Calif., 1974–2017. 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.

Year

2013 2014 2015 2016 2017 

 Percent PercentNon-reproductive Reproductive

-100

-50

0

50

100

Figure 18. Reproductive activity of the clam Macoma petalum, Palo Alto, Calif., 2013–2017. Values are the 

percent of individuals that were either reproductively inactive (non-reproductive; shown as a negative value) or in 

various stages of reproduction (reproductive; shown as a positive value).
42

Figure 19. Total number of species present at the Palo Alto site, Calif., (A) 1974–2017 and (B) 2013–2017. 

Collections were not made between 1991 and 1998. Cm, centimeters.

A.

B.

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of S

p

e

cie

s / 54c

m2

0

10

20

30

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of S

p

e

cie

s / 54c

m2

0

10

20

30
43

Figure 20. Total average number of individuals present at the Palo Alto site, Calif., (A) 1974–2017 and (B) 2012–

2017. Collections were not made between 1991 and 1998. Cm, centimeters.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 

Num

b

er of In

dividuals / 54c

m2

0

500

1000

1500

2000

2012 2013 2014 2015 2016 2017 

Num

b

er of In

dividuals / 54c

m2

0

500

1000

1500

2000

A.

B.
44

Figure 21. Monthly average abundance of Macoma petalum, Palo Alto, Calif., (A) 1974–2017 and (B) 2013–2017.

Error bars represent standard deviation from three replicate samplings. Collections were not made between 1991 

and 1998. Cm, centimeters.

A.

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

20

40

60

80

100

120

140

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

20

40

60

80

100

120

140
45

Figure 22. Monthly average abundance of Mya arenaria, Palo Alto, Calif., (A) 1974–2017 and (B) 2013–2017.

Error bars represent standard deviation from three replicate samplings. Collections were not made between 1991 

and 1998. Cm, centimeters.

A.

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

10

20

30

40

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

2

4

6

8

10
46

Figure 23. Monthly average abundance of Gemma gemma, Palo Alto, Calif., (A) 1974–2017 and (B) 2013–2017.

Error bars represent standard deviation from three replicate samplings. Collections were not made between 1991 

and 1998. Cm, centimeters.

A

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

500

1000

1500

2000

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

300

600

900
47

Figure 24. Monthly average abundance of Ampelisca abdita, Palo Alto, Calif., (A) 1974–2017 and (B) 2013–2017. 

Error bars represent standard deviation from three replicate samplings. Collections were not made between 1991 

and 1998. Cm, centimeters.

A.

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

250

500

750

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

50

100

150

200

250

300
48

Figure 25. Monthly average abundance of Streblospio benedicti, Palo Alto, Calif., (A) 1974–2017 and (B) 2013–

2017. Error bars represent standard deviation from three replicate samplings. Collections were not made between 

1991 and 1998. Cm, centimeters.

A.

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

150

300

450

600

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

25

50

75

100
49

Figure 26. Monthly average abundance of Grandiderella japonica, Palo Alto, Calif., (A) 1974–2017 and (B) 2013–

2017. Error bars represent standard deviation from three replicate samplings. Collections were not made between 

1991 and 1998. Cm, centimeters.

A.

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

20

40

60

80

100

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

10

20

30

40
50

Figure 27. Monthly average abundance of Atilla succinea, Palo Alto, Calif., (A) 1974–2017 and (B) 2013–2017.

Error bars represent standard deviation from three replicate samplings. Collections were not made between 1991 

and 1998. Cm, centimeters.

A.

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

5

10

15

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

5

10

15
51

Figure 28. Monthly average abundance of Heteromastus filiformis, Palo Alto, Calif., (A) 1974–2017 and (B) 2013–

2015. Error bars represent standard deviation from three replicate samplings. Collections were not made between 

1991 and 1998. Cm, centimeters.

A.

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

20

40

60

80

2013 2014 2015 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

10

20

30

40
52

Figure 29. Monthly average abundance of Nippoleucon hinumensis, Palo Alto, Calif., (A) 1974–2017 and (B) 

2013–2017. Error bars represent standard deviation from three replicate samplings. Collections were not made 

between 1991 and 1998. Cm, centimeters.

A.

B.

1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

200

400

600

800

2013 2014 2015 2016 2017 2018 

N

u

m

b

er of In

divid

u

als / 54c

m2

0

200

400

600

800
53

Figure 30. Reproductive mode annual abundance with silver (Ag) concentrations (grand mean ± SEM), in 

milligrams per kilogram (mg/kg), in the clam Macoma petalum and in sediment, Palo Alto, Calif., 1974–2017. 

Annual abundance data (in percent) is from August of each year. The reproductive mode of the top 10 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.

Abundanc

e (%)

0

20

40

60

80

100

% spawners 

% brooders 

% oviparous 

% mixed 

Ag in cla

mtissue (mg/kg)

0

20

40

60

80

100

120

140

1970 1980 1990 2000 2010 2020

Ag in sediment (mg/kg)

0.0

0.5

1.0

1.5

2.0

2.5
54

Figure 31. Reproductive mode annual abundance with copper (Cu) concentrations (grand mean ± SEM), in 

milligrams per kilogram (mg/kg), in the clam Macoma petalum and in sediment, Palo Alto, Calif., 1974–2017. 

Annual abundance data (in percent) is from August of each year. The reproductive mode of the top 10 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.

Cu in cla

mtissue (mg/kg)

0

100

200

300

400

1970 1980 1990 2000 2010 2020

Cu in sediment (mg/kg)

0

20

40

60

80

100

120

Abundance (%)

0

20

40

60

80

100

% spawners 

% brooders 

% oviparous 

% mixed 
55

Figure 32. Feeding mode annual abundance with silver (Ag) concentrations, in milligrams per kilogram (mg/kg), in 

the clam Macoma petalum and in sediment, Palo Alto, Calif., 1974–2017. Annual abundance data (in percent) is 

from August of each year. The feeding mode of the top 10 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; carnivore, preys on other infaunal invertebrates.

Abundance (%)

0

20

40

60

80

100

% filter feeders 

% sub-surface feeders 

% surface feeders 

% mixed feeders 

% carnivore 

Ag in cla

mtissue (mg/kg)

0

20

40

60

80

100

120

140

1970 1980 1990 2000 2010 2020

Ag in sediment (mg/kg)

0.0

0.5

1.0

1.5

2.0

2.5
56

Figure 33. Feeding mode annual abundance with copper (Cu) concentrations in the clam Macoma petalum and in 

sediment, Palo Alto, Calif., 1974–2017. Annual abundance data (in percent) is from August of each year. The 

feeding mode of the top 10 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; carnivore, preys on 

other infaunal invertebrates.

Cu in cla

mtissue (mg/kg)

0

100

200

300

400

A

bund

anc

e (%)

0

20

40

60

80

100

% filter feeders 

% sub-surface feeders 

% surface feeders 

% mixed feeders 

% carnivore 

1970 1980 1990 2000 2010 2020

Cu in se

diment (mg/kg)

0

20

40

60

80

100

120
57

Figure 34. Species rank-abundance for the benthic community, Palo Alto, Calif., for 2016 and 2017.

Gemma gemma

Nippoleucon hinumensis

Tubificidae

Potamocorbula ...

Eusarsiella ... Heteromastus ... Ampelisca ... Eteone lighti

Corophium ... Macoma 

petalum

Tubificidae

Gemma gemma

Nippoleucon 

hinumensis

Macoma petalum

Heteromastus 

filiformis

Grandidierella 

japonica

Corophium 

alienense Eteone lighti

Streblospio 

benedicti Monocorophium 

acherusicum

0

1

2

3

4

5

6

1 2 3 4 5 6 7 8 9 10

LOG(N+1) ABUNDANCE

RANK

2016 2017
58

Figure 35. Species rank-abundance identified by feeding mode, Palo Alto, Calif., for 1977, 1989, 2002, and 2017. 

The feeding mode for each species at each rank 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; carnivore, predator 

on other fauna.

Filter

Surface Deposit

Filter

Mixed Carnivore

Mixed Sub-Surface 

Deposit Carnivore

Surface Deposit

Mixed

Surface ...

Sub-Surface 

Deposit

Filter

Filter Sub-Surface Deposit

Carnivore Surface Deposit

Mixed Carnivore

Mixed

Filter

Mixed

Mixed

Sub-Surface Deposit

Sub-Surface 

Deposit Mixed

Carnivore Filter Surface 

Deposit Mixed

Sub-Surface 

Deposit

Filter

Surface Deposit

Mixed Sub-Surface 

Deposit

Carnivore

Mixed Mixed Mixed

Surface Deposit

0

1

2

3

4

5

6

7

1 2 3 4 5 6 7 8 9 10

LOG(N+1) ABUNDANCE

RANK

1977 1989 2002 2017
59

Figure 36. Species rank-abundance data identified by reproductive mode, Palo Alto, Calif., for 1977, 1989, 2002, 

and 2017. 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.

Brooder

Brooder

Brooder

Brooder

Oviparous

Spawner Mixed Spawner

Oviparous

Brooder

Brooder

Mixed

Brooder

Brooder Oviparous Spawner Brooder

Spawner Oviparous

Spawner

Brooder

Brooder

Spawner

Oviparous

Mixed

Spawner

Spawner Spawner Brooder Brooder

Mixed

Brooder

Brooder

Spawner

Oviparous

Spawner

Brooder Brooder Brooder

Brooder

0

1

2

3

4

5

6

7

1 2 3 4 5 6 7 8 9 10

LOG(N+1) OF ABUNDANCE

RANK

1977 1989 2002 2017
60

Table 1. Concentrations of fine particles in surface sediments and major and minor inorganic elements for samples collected from Palo Alto, Calif., 2017. [Units for aluminum (Al), iron (Fe), and fine sediment are percent of dry weight. Fine sediment is operationally determined as ≤100 micrometer grain size. Elemental 

concentrations for the monthly samples are reported as the mean ±1 standard deviation (std) for replicate subsamples (n=2), except mercury (Hg) and selenium (Se) which 

are single measurements (n=1). Units are milligram per kilogram dry weight. 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, except for silver (Ag), which is based on partial extraction (see text section in 

Methods). ND, no data.]

Date

Fine 

sediment 

(%)

Ag Al (%) Cr Cu Fe (%) Hg Ni Se Zn

1/20/2017 47 0.21 ± 0.003 3.9 ± 0.2 108 ± 4 28.6 ± 0.5 3.8 ± 0.1 0.28 76 ± 0.1 0.52 107 ± 0.9

2/16/2017 67 0.23 ± 0.002 4.2 ± 0.3 110 ± 4 31.0 ± 2.2 4.2 ± 0.0 0.27 89 ± 0.2 0.50 119 ± 0.3

3/14/2017 66 0.18 ± 0.002 3.9 ± 0.4 103 ± 6 28.9 ± 0.9 3.7 ± 0.2 ND 77 ± 2.3 ND 102 ± 3.8

4/12/2017 63 0.25 ± 0.001 4.4 ± 0.5 102 ± 19 35.0 ± 2.2 4.3 ± 0.2 0.30 88 ± 0.9 0.52 124 ± 2.5

5/10/2017 45 0.19 ± 0.003 4.4 ± 0.1 118 ± 0 33.2 ± 1.2 4.2 ± 0.0 ND 88 ± 0.1 ND 118 ± 0.0

6/12/2017 31 0.17 ± 0.003 3.3 ± 0.0 98 ± 1 22.7 ± 0.2 3.5 ± 0.0 0.22 71 ± 0.3 0.36 94 ± 1.0

9/6/2017 35 0.18 ± 0.006 3.6 ± 0.3 110 ± 12 31.4 ± 0.5 3.6 ± 0.0 0.29 79 ± 0.4 0.40 109 ± 0.8

10/18/2017 44 0.25 ± 0.004 7.4 ± 0.1 214 ± 4 24.7 ± 0.1 7.5 ± 0.2 ND 159 ± 3.5 ND 109 ± 2.3

12/11/2017 76 0.21 ± 0.001 4.9 ± 0.1 118 ± 5 34.2 ± 0.3 4.3 ± 0.0 0.35 97 ± 0.2 0.48 127 ± 0.1

Annual Mean: 53 0.21 4.4 120 30 4.3 0.29 92 0.46 112

SEM: 5 0.01 0.4 12 1 0.4 0.02 9 0.03 4
61

Table 2. Concentrations of trace metals and the condition index of the clam Macoma petalum, Palo Alto, Calif., 2017. [Monthly data are the mean and standard deviation for replicate composites (n=8–11, n=2–3 for selenium [Se] and mercury [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 (CI) is the soft tissue weight in milligrams of a clam of 25-millimeter shell length. ND, no data]

Date Ag Cr Cu Hg Ni Se Zn Condition 

index

1/20/2017 3.4 ± 0.3 3.41 ± 0.45 60 ± 8 0.42 ± 0.05 5.6 ± 0.4 4.56 ± 0.60 272 ± 29 73

2/16/2017 4.1 ± 0.5 5.16 ± 0.03 100 ± 25 0.48 ± 0.05 6.9 ± 0.5 4.84 ± 0.30 337 ± 27 64

3/14/2017 5.4 ± 1.0 4.74 ± 0.41 124 ± 20 ND 7.6 ± 0.7 ND 511 ± 41 68

4/12/2017 3.8 ± 0.2 2.52 ± 0.19 120 ± 9 0.59 ± 0.16 4.6 ± 0.2 4.88 ± 0.10 305 ± 11 108

5/10/2017 3.4 ± 0.5 1.58 ± 0.11 100 ± 20 ND 4.1 ± 0.1 ND 335 ± 18 108

6/12/2017 3.2 ± 0.2 1.65 ± 0.06 78 ± 12 0.51 ± 0.09 4.7 ± 0.1 4.82 ± 0.30 357 ± 27 105

9/6/2017 5.8 ± 0.5 2.41 ± 0.17 121 ± 17 0.71 ± 0.10 5.6 ± 0.3 5.12 ± 0.20 345 ± 16 85

10/18/2017 4.9 ± 0.5 4.61 ± 0.36 124 ± 0 ND 6.0 ± 0.2 ND 331 ± 21 89

12/11/2017 5.3 ± 1.1 3.70 ± 0.59 117 ± 44 0.70 ± 0.17 5.6 ± 0.9 5.56 ± 0.20 326 ± 53 262

Annual mean: 4.37 3.31 105 0.57 5.64 4.96 346 107

SEM: 0.34 0.45 8 0.05 0.37 0.14 22 20
62

Appendix 1. Certified concentrations and the percent recoveries 

of inorganic elements in National Institute of Science and 

Technology (NIST) Standard Reference Material 2709a (San 

Joaquin Soil) and 2711a (Montana Soil) prepared in 2017.

[mg/kg, milligrams per kilogram; %, percent; CI, 95% confidence interval; N, sample size]

Reference 

material Constituent N

Certified 

value 

(mg/kg)

Recovery mean 

± CI (%)

2709a Aluminum 18 73,700 49 ± 1

Chromium 18 130 65 ± 3

Copper 18 33.9 67 ± 1

Iron 18 33,600 93 ± 1

Nickel 18 85 87 ± 1

Sliver unknown

Zinc 18 103 71 ± 1

2711a Aluminum 18 67,200 41 ± 1

Chromium 18 52.3 52 ± 2

Copper 18 140 82 ± 1

Iron 18 28,200 86 ± 1

Nickel 18 21.7 62 ± 1

Sliver 18 6 89 ± 3

Zinc 18 414 94 ± 1
63

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 2017.

[Samples were not diluted prior to analysis. %, percent, mg/kg, milligrams per kilogram; CI, 95% confidence interval; N, 

sample size]

Reference 

material Constituent N

Certified 

value 

(mg/kg)

Recovery mean 

± CI (%)

Tort-3 Chromium 18 1.95 83 ± 3

Copper 18 497 84 ± 3

Nickel 18 5.3 81 ± 3

Silver unknown

Zinc 18 136 107 ± 2

1566b Chromium unknown

Copper 18 71.6 94 ± 3

Nickel 18 1.04 91 ± 2

Silver 18 0.666 92 ± 5

Zinc 18 1424 110 ± 3

Appendix 3. Mercury (Hg) and selenium (Se) concentrations 

determined in sample splits of surface sediments and Macoma 

petalum collected at Palo Alto, Calif., 2017.

[One sediment sample and one clam tissue sample were split and analyzed for Se and Hg; the split results are shown here. %, 

percent, mg/kg, milligrams per kilogram dry weight; SD, standard deviation; CV, coefficient of variation]

Sample type Constituent Sample Measured 

(mg/kg) Mean SD CV (%)

Sediment Hg 20170412 SeM PAMF SD 0.29 0.30 0.007 2.34

20170412 SeM PAMF SD LDUP 0.31

Se 20170612 SeM PAMF 0.42 0.42 0.007 1.63

20170612 SeM PAMF Dup 0.43

Tissue Hg 20170216 SeM PAMF MPE 2 0.56 0.57 0.005 0.80

20170216 SeM PAMF MPE 2 LDUP 0.57

20170906 SeM PAMF MPE 3 0.82 0.83 0.006 0.71

20170906 SeM PAMF MPE 3 LDUP 0.83

Se 20170216 SeM PAMF MPE 2 3.92 3.92 0.005 0.12

20170216 SeM PAMF MPE Dup 3.93

20170906 SeM PAMF MPE 3.08 3.03 0.049 1.62

20170906 SeM PAMF MPE 2 Dup 2.98
64

Appendix 4. The percent recovery (± 1 standard deviation) of 

mercury (Hg) and selenium (Se) in standard reference materials.

[N, sample size; mg/kg, milligrams per kilogram; SD, standard deviation]

Reference 

material Constituent N

Certified 

value 

(mg/kg)

Recovery mean ± 

SD (%)

TORT3 Hg 3 0.292 85 ± 3

NIST2976 Hg 3 0.061 97 ± 1

Se 3 1.8 104 ± 2

PACS3 Hg 2 3.04 91 ± 0.1

DOLT3 Se 3 7.1 100 ± 1

MESS Se 3 0.72 113 ± 3

Appendix 5. Method detection limits (MDL) and reporting levels 

(MRL) for Inductively Coupled Plasma Optical Emission 

Spectrophotometry (ICP-OES) methods.

[Concentration is reported as milligrams per liter (mg/L)]

Method Ag Al Cr Cu Fe Ni Zn

Sediment MDL 0.0005 0.0196 0.0320 0.0174 0.0162 0.0004 0.0029

MRL 0.0010 0.0392 0.0640 0.0347 0.0324 0.0008 0.0058

Tissue MDL 0.0005 0.0035 0.0030 0.0005 0.0008

MRL 0.0010 0.0071 0.0060 0.0011 0.0015
65

Appendix 6. Correlation matrix of percent of fine-grained particles (<100 

micrometers [μm]) and chemical properties of surficial sediment based on monthly 

means of all samples collected at Palo Alto, Calif., during the period 1994–2017 

(except total organic carbon [TOC] 1994–2016). 

[Monthly data represent the general seasonal pattern. Data were standardized for the analysis. Correlation coefficients in bold type are significant (p<0.05). 

Original mass concentration was reported in milligrams per kilogram (mg/kg), except Al, Fe, and TOC, which were reported in percent (%). Partially extractable 

Ag, Cu, and Zn are indicated by the subscript p-extract. Data for TOC cover the period 1994–2016]

Variable % <100 

μm Agp-extract Al % Cr Cup-extract Cu Fe (%) Hg Ni Se Znp-extract Zn TOC

% <100 um 1.00

Agp-extract 0.93 1.00

Al % 0.93 0.96 1.00

Cr 0.90 0.94 0.99 1.00

Cup-extract 0.91 0.95 0.95 0.93 1.00

Cu 0.92 0.96 0.98 0.97 0.99 1.00

Fe % 0.87 0.96 0.95 0.96 0.96 0.97 1.00

Hg 0.39 0.56 0.41 0.43 0.48 0.48 0.61 1.00

Ni 0.91 0.96 0.98 0.98 0.94 0.97 0.99 0.56 1.00

Se 0.90 0.96 0.94 0.93 0.98 0.98 0.96 0.56 0.95 1.00

Znp-extract 0.94 0.95 0.95 0.93 0.99 0.99 0.95 0.50 0.95 0.97 1.00

Zn 0.87 0.92 0.95 0.95 0.95 0.97 0.96 0.54 0.97 0.96 0.96 1.00

TOC 0.91 0.92 0.95 0.95 0.99 0.98 0.94 0.39 0.93 0.97 0.97 0.94 1.00
66

Appendix 7. Statistical summary of silver (Ag) and copper (Cu)

concentrations in sediment and the clam Macoma petalum, Palo 

Alto, Calif., for 2017 and 1977–2017.

[Mean, median, minimum, and maximum are calculated from all data from 1977–2017. The 2017 column presents data for 

the calendar year. Values for the 2017 column are annual (grand) means and the standard errors of those means. The other 

columns are statistics from the grand means of 1977–2017. Samples were collected between January and December of each 

year. 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 2017 Mean Median Min Max

Sediment Ag partial extraction 0.21 ± 0.01 0.49 0.35 0.20 1.6

Cu partial extraction 14 ± 1 22 19 12 55

Cu near total 30 ± 1 44 43 30 86

M. petalum Ag tissue digest 4.4 ± 0.3 23 4 2 106

Cu tissue digest 105 ± 8 76 43 24 287

Appendix 8. Reproduction data for Macoma petalum, Palo Alto, 

Calif., 2013–2017.

[Data signify the percentage of clams in each stage of reproduction. Reproductive, the percentage of clams in active, ripe, 

and spawning stages. Non-Reproductive, the percentage of clams in inactive and spent stages. Spent means the clams have 

released all their gametes. N, number of clams that were analyzed; nd, no data]

Date Inactive Active Ripe Spawning Spent N Reproductive Non-Reproductive

16-Jan-13 0.0 30.0 70.0 0.0 0.0 10 100.0 0.0

13-Feb-13 0.0 0.0 100.0 0.0 0.0 10 100.0 0.0

16-Mar-13 0.0 0.0 100.0 0.0 0.0 10 100.0 0.0

16-Apr-13 0.0 0.0 10.0 90.0 0.0 10 100.0 0.0

14-May-13 60.0 0.0 0.0 0.0 40.0 10 0.0 -100.0

12-Jun-13 30.0 0.0 0.0 0.0 70.0 10 0.0 -100.0

1-Jul-13 nd nd nd nd nd nd nd nd

1-Aug-13 nd nd nd nd nd nd nd nd

13-Sep-13 50.0 50.0 0.0 0.0 0.0 10 50.0 -50.0

22-Oct-13 10.0 80.0 10.0 0.0 0.0 10 90.0 -10.0

1-Nov-13 nd nd nd nd nd nd nd nd

10-Dec-13 0.0 10.0 90.0 0.0 0.0 10 100.0 0.0

8-Jan-14 0.0 30.0 70.0 0.0 0.0 10 100.0 0.0

4-Feb-14 0.0 0.0 100.0 0.0 0.0 10 100.0 0.0

4-Mar-14 0.0 0.0 90.0 10.0 0.0 10 100.0 0.0

2-Apr-14 0.0 0.0 10.0 90.0 0.0 10 100.0 0.0

6-May-14 10.0 0.0 10.0 80.0 0.0 10 90.0 -10.0

17-Jun-14 30.0 0.0 0.0 0.0 70.0 10 0.0 -100.0
67

Date Inactive Active Ripe Spawning Spent N Reproductive Non-Reproductive

1-Jul-14 nd nd nd nd nd nd nd nd

1-Aug-14 nd nd nd nd nd nd nd nd

9-Sep-14 10.0 90.0 0.0 0.0 0.0 10 90.0 -10.0

17-Oct-14 60.0 40.0 0.0 0.0 0.0 10 40.0 -60.0

1-Nov-14 nd nd nd nd nd nd nd nd

2-Dec-14 0.0 70.0 30.0 0.0 0.0 10 100.0 0.0

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

28-Oct-15 10.0 70.0 20.0 0.0 0.0 10 90.0 -10

1-Nov-15 nd nd nd nd nd nd nd nd

21-Dec-15 0.0 0.0 100.0 0.0 0.0 10 100.0 0

19-Jan-16 0.0 0.0 100.0 0.0 0.0 10 100 0

16-Feb-16 0.0 0.0 60.0 40.0 0.0 10 100 0

30-Mar-16 10.0 0.0 20.0 40.0 30.0 10 60 -40

27-Apr-16 0.0 0.0 40.0 50.0 10.0 10 90 -10

31-May-16 0.0 0.0 0.0 20.0 80.0 10 20 -80

21-Jun-16 0.0 0.0 0.0 10.0 90.0 10 10 -90

1-Jul-16 nd nd nd nd nd nd nd

1-Aug-16 nd nd nd nd nd nd nd

19-Sep-16 0.0 60.0 40.0 0.0 0.0 10 100 0

17-Oct-16 0.0 70.0 30.0 0.0 0.0 10 100 0

1-Nov-16 nd nd nd nd nd nd nd

19-Dec-16 0.0 10.0 90.0 0.0 0.0 10 100 0

20-Jan-17 0.0 0.0 70.0 30.0 0.0 10 100.0 0

16-Feb-17 0.0 0.0 100.0 0.0 0.0 10 100.0 0

14-Mar-17 0.0 0.0 100.0 0.0 0.0 10 100.0 0

12-Apr-17 0.0 0.0 20.0 80.0 0.0 10 100.0 0

10-May-17 0.0 0.0 0.0 40.0 60.0 10 40.0 -60

12-Jun-17 30.0 30.0 0.0 0.0 40.0 10 30.0 -70

1-Jul-17 nd nd nd nd nd nd nd nd

1-Aug-17 nd nd nd nd nd nd nd nd

6-Sep-17 40.0 60.0 0.0 0.0 0.0 10 60.0 -40

18-Oct-17 0.0 30.0 60.0 10.0 0.0 10 100.0 0

1-Nov-17 nd nd nd nd nd nd nd nd

11-Dec-17 0.0 33.3 55.6 11.1 0.0 9 100.0 0
68

Appendix 9. Complete list of benthic species found at Palo Alto in the year 2017.

[Three samples are taken at each sampling event. The mean (σ) and standard deviation (SD) of the three samples are shown]

Taxon 1/9/2017 2/7/2017 3/6/2017 4/12/2017 5/11/2017 6/9/2017 7/11/2017 8/24/2017 9/7/2017 10/5/2017

σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD

PHYLUM CNIDARIA

Class Anthozoa

Order Actiniaria

Actiniaria spp. 1.7 1.5 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

Class Hydrozoa

Hydrozoa 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 PLATYHELMINTHES

Class Turbellaria

Turbellaria 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 NEMATODA

Nematoda 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 ANNELIDIA

Class Clitellata

Naididae 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 spp. 37.7 20.7 136.3 77.2 56.3 41.1 153.7 29.4 54.0 24.9 54.3 44.1 4.0 6.9 93.7 56.4 23.3 28.9 15.0 12.5

Class Polychaeta

Order Eunicida

Family Dorvilleidae

Schistomeringos 

longicornis

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Schistomeringos 

annulata

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Family Eunicidae

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

Family Lumbrineridae

Scoletoma luti 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Order Phyllodocida

Family Glyceridae

Glycera 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

Family Goniadidae

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
69

Taxon 1/9/2017 2/7/2017 3/6/2017 4/12/2017 5/11/2017 6/9/2017 7/11/2017 8/24/2017 9/7/2017 10/5/2017

σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD

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 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 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

Family Nephtyidae

Nephtys caecoides 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Nephtys 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 0.0 0.0

Family Nereididae

Alitta succinea 0.0 0.0 0.3 0.6 0.7 1.2 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.3 0.6 0.0 0.0 0.3 0.6

Family Phyllidocidae

Eteone 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

Eteone lighti 5.7 2.5 4.0 1.7 4.0 2.6 1.7 2.1 7.7 1.5 2.3 0.6 2.7 2.1 3.3 4.2 1.3 1.5 2.3 1.2

Phyllodoce 

williamsi

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Family Polynoidae

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

Family Syllidae

Exogone lourei 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 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

Syllidae 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

Typosillis 

nipponica

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Infraclass Scolecida

Family Capitellidae

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

Heteromastus 

filiformis

8.3 1.2 5.0 1.0 5.7 3.2 7.7 1.2 5.0 2.6 4.0 3.5 4.0 2.6 7.3 5.1 5.0 5.6 4.3 1.5

Family Cossuridae

Cossura 

pygodactylata

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Family Maldanidae

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

Family Orbiniidae

Leitoscoloptlos 

pugettensis

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Leitoscoloplos 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
70

Taxon 1/9/2017 2/7/2017 3/6/2017 4/12/2017 5/11/2017 6/9/2017 7/11/2017 8/24/2017 9/7/2017 10/5/2017

σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD σ SD

Order Sabellida

Family Sabellidae

Euchone limnicola 1.7 1.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Laonome calida 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Laonome 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

Order Spionida

Family Spionidae

Boccardia 

pugettensis

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Boccardiella 

ligerica

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Dipolydora 

brachycephala

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Dipolydora socialis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

Dipolydora 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

Marenzelleria 

neglecta

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 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 0.0 0.0

Polydora limicola 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 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 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 0.3 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

Pseudopolydora 

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

Spionidae 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

Streblospio 

benedicti

0.7 0.6 1.0 1.0 6.3 11.0 17.3 11.7 17.3 9.7 9.0 11.3 0.7 1.2 3.3 2.5 1.0 1.7 0.0 0.0
71

Appendix 10. Benthic species name changes as of 2017.

Current Species Name Formerly Document As

PHYLUM CNIDARIA

Class Anthozoa

Order Actiniaria

Actiniaria spp. Anthozoa, Unid. Actiniaria, Actiniaria unid. spp.

PHYLUM PLATYHELMINTHES

Class Turbellaria

Turbellaria spp. Turbellaria, Turbellaria unid. spp.

PHYLUM NEMATODA

Nematoda spp. Nematoda unid. spp.

PHYLUM ANNELIDA

Class Clitellata

Naididae spp. Naididae, Naididae unid. spp.

Oligochaeta spp. Oligochaeta, Unid. Oligochaeta family, 

Oligochaeta unid. spp.

Class Polychaeta

Polychaeta spp. Unid. Polychaeta, Polychaeta, Polychaeta unid. 

spp.

Order Eunicida

Family Dorvilleidae

Schistomeringos longicornis Dorvillea longicornis

Schistomeringos annulata Dorvillea annulata, Dorvillea longicornuta, 

Schistomeringos longicornuta, Dorvillea rudolphi

Order Phyllodocida

Family Glyceridae

Glycera spp. Glycera unid. spp.

Family Goniadidae

Glycinde picta Glycinde polygnatha

Glycinde sp. SF1 Glycinde unid. Sp. SF1

Glycinde spp. Glycinde unid. Spp.

Family Nereididae

Alitta succinea Neanthes succinea

Family Phyllidocidae

Eteone spp. Eteone ? Californica, Eteone unid. spp.

Family Syllidae

Sphaerosyllis unid. sp. A Sphaerosylis spp.

Infraclass Scolecida

Family Capitellidae

Capitella capitata complex Capitella “capitata”

Family Maldanidae

Maldanidae spp. Unid. Maldanidae, Maldanidae unid. spp.

Order Sabellida

Family Sabellidae

Euchone spp. Euchone unid. spp.

Order Spionida

Family Spionidae

Polydora cornuta Polydora lighti, Polydora ligni

Polydora spp. Polydora unid. Spp.

Spionidae spp. Unid. Spionidae, Spionidae Unidentified, Spionidae

unid. Spp.
72

Current Species Name Formerly Document As

Order Terebellida

Family Cirratulidae

Cirratulidae spp. Tharyx spp. ?, Cirratulidae, Cirratulidae unid. Spp.

PHYLUM ARTHROPODA

Class Insecta

Chironomidae spp. Chironomidae, Chironomidae unid. spp.

Class Maxillopoda

Calanoida spp. Calanoida, Calanoida unid. spp.

Harpacticoida spp. Harpacticoida, Harpacticoida unid. spp.

Class Gastropoda

Gastropod unid. sp. B Unidentified Gastropoda B

Order Cephalaspidea

Family Philinidae

Philine spp. Philine unid. spp.

Order Heterostropha

Family Pyramidellidae

Odetta bisuturalis Boonea bisuturalis, Odostomia fetella

Pyramidellidea spp. Odostomia spp., Pyramidellidea, Unidentified 

Gastropod A, Pyramidellidae unid. spp.

Family Nassariidea

Ilyanassa obsoleta Nassarius obsoletus
ISSN 2331-1258 (online)

https://doi.org/10.3133/

ofr20181107