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: 2005 

U.S. GEOLOGICAL SURVEY 

OPEN FILE REPORT 2006-1152 

Prepared in cooperation with the 

CITY OF PALO ALTO, CALIFORNIA

Menlo Park, California 
i

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: 2005 

Daniel J. Cain, Francis Parchaso, Janet K. Thompson, Samuel N. Luoma, 

Allison H. Lorenzi, Edward Moon, Michelle K. Shouse, Michelle I. 

Hornberger, and Jessica L. Dyke 

U.S. GEOLOGICAL SURVEY 

OPEN FILE REPORT 2006-1152 

Prepared in cooperation with the 

CITY OF PALO ALTO, CALIFORNIA 
ii
iii

U.S. DEPARTMENT OF THE INTERIOR 

LYNN SCARLETT, Acting Secretary 

U.S. GEOLOGICAL SURVEY 

PATRICK LEAHY, Acting Director 

Any use of trade, firm, or product names is for descriptive purposes only and does not imply 

endorsement by the U.S. Government. 

For Additional Information 

Write to: snluoma@usgs.gov 

Copies of this report may be 

obtained from the authors,

on the Web at: 

http://pubs.water.usgs.gov/ofr2006-1152

Samuel N. Luoma, MS 465 

U.S. Geological Survey 

345 Middlefield Road 

Menlo Park, CA 94025 

or U.S. Geological Survey 

Information Center 

Box 25286, MS 517

Denver Federal Center 

Denver, CO 80225
iv

Table of contents 

Abstract.........................................................................................................................................1

Introduction ...................................................................................................................................2

Environmental Monitoring...........................................................................................................2

RWQCB and NPDES .................................................................................................................3

Objectives ..................................................................................................................................3

Approach....................................................................................................................................4

Study Site...................................................................................................................................5

Methods ........................................................................................................................................5

Sampling Frequency ..................................................................................................................5

Measurements of Metal Exposure..............................................................................................6

Biological Response...................................................................................................................9

Results and Discussion.................................................................................................................9

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

Sediments ................................................................................................................................10

Clam Tissue .............................................................................................................................11

Reproduction of Macoma petalum ..............................................................................................12

Benthic Community ..................................................................................................................13

Summary.....................................................................................................................................14

Long-term Observations...........................................................................................................14

2005 .........................................................................................................................................16

Value of Long-Term Monitoring................................................................................................16

References..................................................................................................................................17

Figures ........................................................................................................................................21

Tables .........................................................................................................................................66

Appendix A..................................................................................................................................72

Appendix B..................................................................................................................................76

Appendix C..................................................................................................................................87

Appendix D................................................................................................................................106

Appendix E................................................................................................................................109

Appendix F................................................................................................................................113

Appendix G ...............................................................................................................................115

Appendix H................................................................................................................................117
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List of figures 

Figure 1. Location of the Palo Alto sampling site in South San Francisco Bay. ..........................22

Figure 2. Precipitation .................................................................................................................23

Figure 3. Water column salinity ...................................................................................................24

Figure 4. Aluminum, iron and silt/clay in sediments ....................................................................25

Figure 5. Chromium, nickel and vanadium in sediments.............................................................26

Figure 6. Copper in sediments ....................................................................................................27

Figure 7. Zinc in sediments .........................................................................................................28

Figure 8. Silver in sediments .......................................................................................................29

Figure 9. Selenium and mercury in sediments ............................................................................30

Figure 10. Annual mean copper in Macoma petalum..................................................................31

Figure 11. Annual mean silver in Macoma petalum ....................................................................32

Figure 12. Copper in Macoma petalum .......................................................................................33

Figure 13. Silver in Macoma petalum..........................................................................................34

Figure 14. Chromium in Macoma petalum ..................................................................................35

Figure 15. Nickel in Macoma petalum .........................................................................................36

Figure 16. Zinc in Macoma petalum ............................................................................................37

Figure 17. Mercury in Macoma petalum......................................................................................38

Figure 18. Selenium in Macoma petalum....................................................................................39

Figure 19. Condition index of Macoma petalum ..........................................................................40

Figure 20. Reproductive activity of Macoma petalum..................................................................41

Figure 21. Reproductive activity of Macoma petalum 2000 thru 2005.........................................42

Figure 22. Total number of species present................................................................................43

Figure 23. Total average number of individuals present..............................................................44

Figure 24. Average abundance of Macoma petalum...................................................................45

Figure 25. Average abundance of Mya arenaria .........................................................................46

Figure 26. Average abundance of Gemma gemma ....................................................................47

Figure 27. Average abundance of Ampelisca abdita...................................................................48

Figure 28. Average abundance of Streblospio benedicti.............................................................49

Figure 29. Average abundance of Grandiderella japonica ..........................................................50

Figure 30. Average abundance of Neanthes succinea................................................................51

Figure 31. Average abundance of Heteromastus filiformis..........................................................52

Figure 32. Average abundance of Nippoleucon hinumensis .......................................................53

Figure 33. Heteromastus filiformis abundance with silver and copper in Macoma 

petalum. ......................................................................................................................................54

Figure 34. Heteromastus filiformis annual abundance with silver in M. petalum and 

sediment......................................................................................................................................55

Figure 35. Heteromastus filiformis annual abundance with copper in M. petalum and 

sediment......................................................................................................................................56

Figure 36. Ampelisca abdita abundance with silver and copper in M. petalum ...........................57

Figure 37. Ampelisca abdita annual abundance with silver in M. petalum and sediment............58

Figure 38. Ampelisca abdita annual abundance with copper in M. petalum and sediment .........59

Figure 39. Streblospio benedicti abundance with silver and copper in M. petalum .....................60

Figure 40. Streblospio benedicti annual abundance with silver in M. petalum and 

sediment......................................................................................................................................61
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Figure 41. Streblospio benedicti annual abundance with copper in M. petalum and 

sediment......................................................................................................................................62

Figure 42. Gemma gemma abundance with silver and copper in M. petalum.............................63

Figure 43. Gemma gemma annual abundance with silver in M. petalum and sediment..............64

Figure 44. Gemma gemma annual abundance with copper in M. petalum and sediment...........65

List of tables 

Table 1. Sediment characteristics and salinity in 2005...............................................................67

Table 2. Concentrations of trace elements in sediments in 2005 ................................................68

Table 3. Annual mean copper in Macoma petalum and sediments 1977 through 2005.............69

Table 4. Annual mean silver in Macoma petalum and sediments 1977 through 2005 ...............70

Table 5. Concentrations of trace elements in Macoma petalum in 2005.....................................71

Conversion Factors, Abbreviations, and Acronyms 

Conversion Factors 

Multiply By To obtain 

foot (ft) 0.3048 meter 

gallon (gal) 3.785 liter (L) 

inch (in.) 2.54 centimeter 

inch (in.) 25,400 micrometer (μm) 

micromolar (μM) molecular weight micrograms per liter 

micron (μm) 1,000,000 meter 

mile (mi) 1.609 kilometer 

ounce (oz) 28.35 gram (g) 

part per million 1 microgram per gram 

(μg/g) 

Temperature in degrees Celsius (o C) is converted to degrees Fahrenheit (o F) with the following 

equation: 

o F = (1.8 x o C) + 32 
vii

Abbreviations and Acronyms 

Abbreviations and 

Acronyms Meaning 

CI Condition Index 

ERL Effects Range-Low 

ERM Effects Range-Median 

ICP-OES Inductively Coupled Plasma-Optical Emission Spectrophotometry 

IRMS Isotopic Ratio Mass Spectrophotometry 

MDL Method Detection Limit 

MLLW Mean Low Low Water 

MRL Method Reporting Level 

NIST National Institute of Standards and Technology 

NPDES National Pollutant Discharge Elimination System 

PARWQCP Palo Alto Regional Water Quality Control Plant 

RWQCB California Regional Water Quality Control Board 

SFEI San Francisco Estuary Institute 

USEPA U.S. Environmental Protection Agency 

USGS U.S. Geological Survey 
1

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: 2005 

Daniel J. Cain, Francis Parchaso, Janet K. Thompson, Samuel N. Luoma, Allison H. 

Lorenzi, Michelle Shouse, Michelle I. Hornberger, and Jessica Dyke 

Abstract 

Trace elements in sediment and the clam Macoma petalum (formerly reported as 

Macoma balthica (Cohen and Carlton 1995)), clam reproductive activity and benthic, 

macroinvertebrate community structure are reported for a mudflat one kilometer south of the 

discharge of the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay. 

This report includes data collected for the period January to December 2005, and extends a 

critical long-term biogeochemical record dating back to 1974. These data serve as the basis for 

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

Metal concentrations in both sediments and clam tissue during 2005 were consistent with 

results observed since 1990. Copper and zinc concentrations in sediment and bivalve tissue 

displayed a continued decrease over the last decade. In 2005, Cu concentrations were at or below 

the effects range-low (ERL) concentration (34 μg/g) for the entire year, the first time this has 

been observed. Also, zinc concentrations never exceeded the ERL (150 μg/g). Yearly average 

concentrations of copper, zinc and silver in Macoma petalum for 2005 were some of the lowest 

recorded since monitoring for metals began in 1975. The concentrations of mercury and 

selenium in sediments, during April and January 2004, respectively, were the highest values 

observed for these elements during this study. Later in 2005, concentrations decreased to historic 

levels. The increase in mercury and selenium in 2004 was not a permanent trend and 

concentrations of these elements in sediments and clams at Palo Alto remain similar to 

concentrations observed elsewhere in the San Francisco Bay. 

Analyses of the benthic-community structure of a mudflat in South San Francisco Bay 

over a 31-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 biosentinal clam 

Macoma petalum from the same area. Analysis of the reproductive activity 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 with almost all animals 

initiating reproduction in the fall and spawning the following spring of most years. The 

community has shifted from being dominated by several opportunistic species to a community 

where the species are more similar in abundance, a pattern that suggests a more stable 
2

community that is subjected to less stress. 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. Heteromastus filiformis, a subsurface polychaete worm that lives in the sediment, 

consumes sediment and organic particles residing in the sediment, and reproduces by laying their 

eggs on or in the sediment has shown a concurrent increase in dominance. These changes in 

species dominance reflect a change in the community from one dominated by surface dwelling, 

brooding species to one with species with varying life history characteristics. For the first time 

since its invasion in 1986, the non-indigenous filter-feeding bivalve Corbula (Potamocorbula) 

amurensis has shown up in small but persistent numbers in the benthic community. 

Introduction 

Environmental Monitoring 

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

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

the basis for inferring ecological implications of metal contamination. 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 response of resident species to environmental conditions, although the underlying cause(s) 

for the response may be difficult to identify and quantify. Integrating measurements of metal 

exposure and biological response can provide a more complete view of anthropogenic 

disturbances and the associated effects on ecosystem health. 

Environmental Exposure to Trace Metals 

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

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

concentrations of metals in sediments serve as a record of metal contamination in an estuary, 

with some integration over time. Fluctuations in the record may be indicative of changes in 

anthropogenic releases of metals into the environment. 

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

metals through contact with and ingestion of bottom sediments and suspended particulate 

materials. However, geochemical conditions of the sediment affect the biological availability of 

the bound metals. Assimilation of bioavailable sediment-bound metal by digestive processes and 

the relative contribution of this source of metals relative to metals in the aqueous phase are not 

well understood. Thus, in order to better estimate bioavailable metal exposures, the tissues of the 

organisms themselves may be analyzed for trace metals. Benthic organisms concentrate most 

metals to levels higher than those that occur in solution. Therefore, the record of tissue metal 

concentrations can be a more sensitive indicator of anthropogenic metal inputs than the sediment 

record. Different species concentrate metals to different degrees. However, if one species is 

analyzed consistently, the results can be employed to indicate trace-element exposures to the 

local food web. For example, silver (Ag), copper (Cu) and selenium (Se) contamination, 

originally observed in clams (Macoma petalum formerly reported as Macoma balthica (Cohen 

and Carlton 1995)) at the Palo Alto mudflat, was later found in diving ducks, snails, and mussels 

also from that region (Luoma and others, USGS, unpublished data). 
3

Biological Response to Trace Metals 

Contaminants can adversely impact benthic organisms at several organizational levels. 

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

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

success. Community level responses to population level impairment can include overall shifts in 

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

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

ultimately result in changes at the ecosystem level due to that community’s importance in the 

cycling of carbon in aquatic environments (see Alpine and Cloern 1992 for 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 (see Wang and Fisher 1999 for a 

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

to contaminant concentration as well as duration. Even at low contaminant levels, long-term 

exposure can impact benthic organisms. The added complexity of synergistic or antagonistic 

effects between different contaminants and between contaminants and natural stressors makes 

the determination of 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 which link changes in exposure at multiple time scales (in this case 

seasonal to decadal) to changes at individual, population and community level. 

RWQCB and NPDES 

The California Regional Water Quality Control Board (RWQCB) has prescribed a Self 

Monitoring Program with its re-issuance of the National Pollutant Discharge Elimination System 

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

specific receiving water monitoring requirements. 

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

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

petalum at an inshore location in South San Francisco Bay. In addition to the required 

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

monitoring protocols have been designed to be compatible with or complement the RWQCB’s 

Regional Monitoring Program. Monitoring efforts are being conducted by the U. S. Geological 

Survey (USGS) and are coordinated with 30 years of previous data collections and investigations 

by the USGS at this inshore location. 

Objectives 

The data presented by this study includes trace-metal concentrations in sediments and 

clams, clam reproductive activity and benthic-community structure. These data, and those 

collected in earlier studies, (Hornberger and others 2000a; Luoma and others 1991; 1992; 1993; 

1995; 1996; 1997; 1998; Wellise and others 1999; David and others 2002; Moon and others 

2003; 2004; Shouse and others 2003; 2004; Thompson and others 2002) 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 
4

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

of other locations in San Francisco Bay published in the international literature 

 Coordinate inshore receiving water monitoring programs for PARWQCB and provide data 

compatible with relevant aspects of the Regional Monitoring Program. The near-field data 

will augment the Regional Monitoring Program as suggested by the RWQCB 

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

development of sediment quality standards. 

Approach 

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

has been effective in relating changes in near-field contamination to changes in reproductive 

activity of a clam (Hornberger and others 2000b) and in benthic-community structure (Kennish 

1998). This study, with its basis in historical data, provides a context within which future 

environmental changes can be assessed. 

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

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

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

affected by hydrology and geochemical factors (Thomson-Becker and Luoma 1985; Luoma and 

others 1995). Thus, ancillary data, including grain-size distribution, organic carbon, aluminum 

and iron content of the sediment, regional rainfall, and surface salinity, were collected to 

interpret seasonal, annual, and inter-annual variation in metal concentrations. The tissue of 

Macoma 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 Macoma petalum were compared with physiological 

indicators. Two common animal responses to environmental stress are reduced reproductive 

activity and reduced growth. 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. Reproductive tissue increases during the early stages 

of reproduction, and subsequently declines during and after reproduction. These cycles can be 

followed with the condition index (CI) which is an indicator of the physiological condition of the 

animal, and specifically is the total soft tissue weight of a clam standardized to shell length. 

Inter-annual differences in growth and reproduction, expressed in the CI, are influenced by the 

availability and quality of food, as well as other stressors such as pollutant exposure and salinity 

extremes. Earlier studies (Hornberger and others 2000b) have shown that reproductive activity 

of M. petalum has increased with declining metal concentrations in animals from this location. 

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

physiological stress by pollutants at this location, and continue to be monitored for 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 

1995) and that some crustacean and polychaete species are particularly sensitive to elevated 

sedimentary copper (Morrisey and others 1996, Rygg 1985). Finally, the benthic community was 

examined for changes in structure (that is, shifts in the species composition of the 

macroinvertebrate community and abundance of individual species at this site). Prior studies 

have shown that more opportunistic species are likely to persist in highly disturbed environments 
5

(see Nichols and Thompson 1985a). It was hypothesized that a shift in community composition 

would result from changes in the concentrations of specific metals or in the composite of all 

contaminants. 

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

community and measured environmental parameters (i.e. salinity, air and water temperature, 

delta outflow, precipitation, chlorophyll a, sediment total organic carbon, and biological oxygen 

demand: Shouse 2002). Therefore, the community data was only compared to trace-metal data 

in this report. 

Study Site 

The Palo Alto site (PA) is located off of Sand Point on a mudflat on the western shore 

side of San Francisco Bay (not a slough) (Figure 1). The site is one kilometer south of the 

intertidal discharge point of the PARWQCP. The station is 12 m from the edge of the marsh and 

110 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 and thereby influence 

the mudflats in the vicinity of Sand Point. Spatial distributions of metal concentrations near the 

PARWQCP site were described by Thomson and others (1984) (also reported by Hornberger and 

others 2000a; Luoma and others 1991; 1992; 1993; 1995; 1996; 1997; 1998; Wellise and others 

1999; David and others 2002; Moon and others 2003; 2004; Shouse and others 2003; 2004; 

Thompson and others 2002). Earlier work by Thomson and others (1984) showed that San 

Francisquito Creek and the Yacht Harbor were minor sources of most trace elements compared 

to the PARWQCP. The PARWQCP appeared to be the primary source of the elevated metal 

concentrations at the PA site in the spring of 1980, based upon spatial and temporal trends of Cu, 

Ag and zinc (Zn) in clams and sediments (Thomson and others 1984; Cain and Luoma 1990). 

Metal concentrations in sediments and clams (M. petalum), especially Cu and Ag, have declined 

substantially since the original studies as more efficient treatment processes and source control 

were employed (Hornberger and others 2000b). Frequent sampling each year was necessary to 

characterize those trends since there was significant seasonal variability (Cain and Luoma 1990; 

Luoma and others 1985). This report characterizes data for the year 2005, employing the 

methods described in the succeeding section. 

Previous reports (Luoma and others 1995; 1996; 1997; 1998; Wellise and others 1999) 

also included data for a site in South Bay that that was influenced by discharge from the San 

Jose/Santa Clara Water Pollution Control Plant (SJ). Samples were collected from this site from 

1994 to September 1999. Comparison of data from this site and the Palo Alto site allowed 

differentiation of local and regional long-term metal trends. 

Methods 

Sampling Frequency 

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

anthropogenic stressors are difficult to distinguish from natural seasonal changes. Frequent 

sampling increases the probability that anthropogenic effects can be identified. Analyses of early 
6

data (1974 through 1983; Nichols and Thompson 1985a, 1985b) showed that when differences 

are small, benthic samples need to be collected at monthly to bimonthly intervals to make the 

distinction between natural and anthropogenic effects. Therefore, samples were collected, with a 

few exceptions, on a monthly basis from the exposed mudflat at low tide between January and 

December 2005. Samples collected in the field included surface sediment, the deposit-feeding 

clam M. petalum, surface water, and sediment cores for community analysis. Surface water, 

surface sediment and M. petalum were not collected during the months of July, August and 

November. Cores for benthic-community analyses were collected during all months except 

October and December.

Measurements of Metal Exposure 

Sediment 

Sediment samples were scraped from the visibly oxidized (brownish) surface layers (top 

1-2 cm) of mud. These surface layers represent recently deposited sediments and detritus, or 

sediments affected by recent chemical reaction with the water column. The sediment also 

supports microflora and fauna, a nutritional source ingested by M. petalum. Sediment samples 

were immediately taken to the laboratory and sieved through a 100 μm polyethylene mesh 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 sediment data reported herein were determined from the fraction that passed through the 

sieve (< 100 μm), termed the silt/clay fraction. Previous studies have shown little difference 

between metal concentrations in sieved and unsieved sediments when silt/clay type sediment 

dominates at a site. However, where sand-size particles dominate the bed sediment, differences 

in metal concentrations can be substantial. Sediments in extreme South San Francisco Bay can 

vary spatially and temporally in their sand content (Luoma and others 1995; 1996; 1997; 1998; 

Wellise and others 1999; David and others 2002; Moon and others 2003; 2004 also see SFEI 

1997). Where sand content varies, sieving reduces the likelihood that differences in metal 

concentrations are the result of sampling sediments of different grain size. Some differences 

between the USGS and the Regional Monitoring Program results (SFEI 1997) reflect the bias of 

particle size on the latter’s data. 

To provide a measure of bulk sediment characteristics at a site, and thus provide some 

comparability with bulk sediment determination such as that employed in the Regional 

Monitoring Program – San Francisco Estuary Institute (SFEI 1997), the fraction of sediment that 

did not pass through the sieve (≥100 μm) was determined. This fraction is termed sand fraction. 

Bulk sediment samples were sieved to determine the percent sand and percent silt/clay (<100 

μm) (Appendix A). The percentage of the bulk sediment sample composed of sand-sized 

particles (percent sand) was determined by weighing the fraction of sediment that did not pass 

through the sieve (≥100 μm), dividing that weight by the total weight of the bulk sample, and 

multiplying the quotient by 100. The percentage of silt/clay in the sediment was determined 

similarly by weighing the sediment that passed through the sieve (grain size <100 μm). 

The silt/clay fraction was dried at 60o C, weighed, and then subsampled to provide 

replicates weighing 0.4 to 0.6 gram. These were re-dried (60o C), re-weighed, and then digested 

by hot acid reflux (10 ml of 16 normal (N) nitric acid) until the digest was clear. This method 

provides a ‘near-total’ extraction of metals from the sediment and is comparable with the 

recommended procedures of the U.S. Environmental Protection Agency (USEPA) and with the 

procedures employed in the Regional Monitoring Program. It also provides data comparable to 
7

the historical data available on San Francisco Bay sediments. While near-total analysis does not 

result in 100% recovery of all metals, recent comparisons between this method and more 

rigorous complete decomposition show that trends in the two types of data are very similar 

(Hornberger and others 1999). After extraction, samples were evaporated until dry, then 

reconstituted in dilute hydrochloric acid (10 % or 0.6 N). The hydrochloric acid matrix was 

specifically chosen because it mobilizes silver (Ag) into solution through the creation of Agchloro complexes. Sediment extracts were allowed to equilibrate with the hydrochloric acid 

(minimum of 48 hours) before they were filtered (0.45 μm) into acid-washed polypropylene vials 

for elemental analysis. 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. The extract was pressure 

filtered (0.45 μm) before elemental analysis. 

Organic carbon was determined using a continuous flow isotope ratio mass 

spectrophotometer (IRMS) (Appendix A). Prior to the analysis, sediment samples were acidified 

with 12 N HCl vapor to remove inorganic carbon. 

 Water pooled on the surface of the mudflat was collected in a bottle and returned to the 

lab where it was measured for salinity with a handheld refractometer. 

Clam Tissue 

Macoma petalum were collected by hand on each sampling occasion. Typically, 60-120 

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

the clams were placed into a screw-cap polypropylene container (previously acid-washed) 

containing site water. These containers were used to transport the clams to the laboratory. 

In the laboratory, the clams were removed from the containers and gently rinsed with deionized water to remove sediment. A small amount of mantle water was collected from 

randomly selected clams for the determination of salinity with a refractometer. The salinity of 

the mantle water and the surface water collected from the site (above) were typically within 1 ppt 

(‰) of each other. Only surface water values are reported here. Natural sand-filtered seawater 

(obtained from U.C. Santa Cruz, Long Marine Labs, Santa Cruz, CA) was diluted with deionized water to the measured salinity of the site water. Clams were immersed in this water and 

moved to a constant temperature room (12o C) for 48 hours to allow for the egestion of sediment 

and undigested material from their digestive tracts. Clams were not fed during this depuration 

period. After depuration, the clams were returned to the laboratory and further prepared for 

chemical analysis. 

Elemental analysis, excluding mercury and selenium 

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

digitally. Clams were separated into 1 mm size classes (e.g. 10.0-10.9 mm, 11.0-11.9mm, etc). 

The soft tissues from all of the individuals within a given size class were dissected from the shell 

and collected in pre-weighed 20 mL screw-top borosilicate glass vials to form a single composite 

sample for elemental analysis. The sample for each collection was thus composed of six to ten 

composites, with each composite consisting of 2 to 19 clams of a similar shell length. The vials 

were capped with a glass reflux bulb and transferred to convection oven (70oC). After the tissues 

were dried to constant weight, they were digested by reflux in sub-boiling 16 N nitric. The tissue 

digests were then dried and reconstituted in 0.6 N hydrochloric acid for trace-element analysis. 
8

Analysis for mercury and selenium 

Samples collected in late winter (January and February), spring (April), and summer 

(June and September) were analyzed for total mercury (Hg) and selenium (Se). Approximately 

40 clams were selected from the 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 3-4 composites, each containing a minimum of ~1.25 gram wet weight. To meet this 

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

form broader size classes (3-4 mm). Once the composites were formed, the clams were dissected 

as described above, and the soft tissue was placed into pre-weighed 30 mL screw top 

polycarbonate vials. These vials were closed and transferred to a freezer (-20o C). Once frozen, 

the samples were freeze-dried. After drying, the samples were shipped to the USGS analytical 

laboratory in Atlanta, GA where they were prepared and analyzed for selenium and mercury 

according to the method described by Elrick and Horowitz (1985). 

Analytical 

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

(Fe), nickel (Ni), silver (Ag), vanadium (V) and zinc (Zn) were determined using Inductively 

Coupled Plasma Optical Emission Spectroscopy (ICP-OES). Mercury (Hg) and Selenium (Se) 

were determined in both sediment and clam tissues by Hydride Atomic Absorption 

Spectrophotometry. Analytical results are included in Appendix B, Appendix C, and Appendix D. 

Quality Assurance 

The polypropylene containers used in the field, depuration containers, glass-reflux bulbs, 

and all glassware and plastic used for metal analysis were first cleaned to remove contamination. 

Cleaning consisted of a detergent wash and rinse in de-ionized water, followed with a 1 N nitricacid wash and thorough rinse in double-deionized water (18 MΩ 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 (i.e. all elements except selenium and mercury) 

were accompanied with procedural blanks and standard reference materials issued by the 

National Institute of Standards and Technology (NIST). Analysis was preceded with instrument 

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

during (approximately every 10 samples) and after each analytical run. Analyses of reference 

materials (NIST 2079, San Joaquin soils and NIST 2976, mussel tissue) were consistent for the 

method and generally were within the range of certified values reported by NIST. Recoveries of 

Cd, Ni, and Pb in NIST 2976 tend to be less than the certified concentrations (Appendix E). 

Method detection limits (MDL) and reporting levels (MRL) were determined using the 

procedures outlined by Glaser and others (1981), Childress and others (1999), and USEPA 

(2004) (Appendix F). A full quality-assurance/quality-control plan is available upon request. 

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 D). 

Other data sources 

Precipitation data for San Francisco Bay is reported at San Francisco International 

Airport and was obtained from the California Data Exchange Center 2005. 
9

Biological Response 

Condition Index 

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

relationship 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 

relationship between the average shell length and tissue dry weight of the composites was fit 

with a linear regression, and from that regression the tissue dry weight was predicted for a 

normalized shell length of 25 mm. 

Reproductive Activity 

A minimum of 10 clams of varying sizes (minimum of 5 mm) were processed for 

reproductive activity concurrent with samples for metal analyses. Clams were immediately 

preserved in 10% formalin at the time of collection. The visceral mass of each clam was 

removed in the laboratory, stored in 70% ethyl alcohol, and then prepared using standard 

histological techniques. Tissues were dehydrated in a graded series of alcohol, cleared in toluene 

(twice for one hour each), and infiltrated in a saturated solution of toluene and Paraplast® for 

one hour, and two changes of melted Tissuemat® for one hour each. Samples were embedded in 

Paraplast® in a vacuum chamber and then thin sectioned (10 μm) using a microtome. Sections 

were stained with Harris’ hematoxylin and eosin and examined with a light microscope. Each 

individual was characterized by size (length in mm), sex, developmental stage, and condition of 

gonads, thus allowing each specimen to be placed in one of five qualitative classes of gonadal 

development (previously described by Parchaso, 1993) (Appendix G). 

Community Analysis 

Samples for benthic-community analysis were collected with an 8.5 cm diameter x 20 cm 

deep hand-held core. Three replicate samples were arbitrarily taken, within a square-meter area, 

during each sampling date.

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

and then later preserved in 70% ethanol. Samples were stained with rose bengal solution. All 

animals in all samples were sorted to species level where possible (some groups are still not well 

defined in the bay, such as the oligochaetes), and individuals for each species were enumerated. 

Taxonomic work was performed in conjunction with a private contractor familiar with the 

taxonomy of San Francisco Bay invertebrates (Susan McCormick, Colfax, CA) (Appendix H). S. 

McCormick also compared and verified her identifications with previously identified samples. 

Results and Discussion 

Salinity 

Surface water salinity is related to the seasonal weather pattern in Northern California, 

which is characterized by a winter rainy season defined by months with rainfall amounts greater 

than 0.25 inches (November through April) and a summer dry season (May through October) 

(Figure 2). The 11 year (1994-2005) average annual rainfall is 24.3 inches. At 30.1 inches, 

precipitation for 2005 was one of the wettest years within this period (rainfall in 1998 was 30.2 

inches). Rainfall during March and April of 2005 was especially greater compared to other 

years. 
10

Surface-water salinity typically exhibits a seasonal pattern that is generally the inverse of 

regional rainfall (Figure 3, Table 1). This pattern was again observed in 2005. The salinity 

minimum of 16 parts per thousand (ppt) occurred in April, consistent with the late season 

rainfall, and elevated inflow of freshwater from surface water runoff. Considering the 

cumulative rainfall for the year, the salinity minimum was not as low as in other years of heavy 

rainfall (e.g. 1997-98). This could indicate that in 2005 winter salinity was affected more by 

local runoff than by the large flushing flows from the Sacramento/San Joaquin Rivers. Salinities 

continually increased during the dry season and reached their maximum (26 ppt) in the fall 

(September-November). 

Sediments 

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

periodicity of seasonal patterns. Thomson-Becker and Luoma (1985) suggested that this interannual variation is related to changes in the size distribution of sediment particles caused by 

deposition of fine-grained particles in the winter and their subsequent wind-driven re-suspension 

in the fall. Thomson-Becker and Luoma showed that the composition of surface sediments was 

dominated by fine-grained particles - and accompanied by high Al and Fe concentrations - 

during the period of freshwater input (low salinities through April), reflecting annual terrigenous 

sediment inputs from runoff. Coarser sediments dominated later in the year because the seasonal 

diurnal winds progressively winnow the fine sediments into suspension through the summer. 

This pattern was observed again in 2005 (Figure 4, Appendix A). 

In 2005, the percent of silt/clay in the sediment was at its maximum (95%) in April, 

coincident with prolonged late season rainfall. Aluminum and Fe concentrations varied with the 

percentage of silt/clay-sized particles (Figure 4, Table 1), as described above, reflecting the 

contribution of clays composed of Al and Fe. 

The total organic carbon (TOC) content of the sediments varied modestly during the year, 

coincident with other sedimentary constituents (Table 1). TOC content was highest during the 

winter (January through April values ranged from 1.44 to 1.48 %), after April declined to a 

minimum in September (0.89%), and then increased during the early winter to 1.23%, as of 

December 2005. In light of the most recent data, the exceptionally high value observed in 

October of 2004 (8.1%) appears to have been an anomalous event. 

The metals Cr, Ni and V are highly enriched in some geologic formations within the 

watershed. 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). Inputs of minerals bearing Cr, Ni, 

and V appear to vary seasonally as suggested by the variable concentrations of these metals in 

surface sediments. Typically, maximum concentrations coincide with winter/spring maximums 

in fine sediments, while minimum concentrations occur during the late summer/fall (Figure 5, 

Table 2). The minimum Ni concentration in the fall of 2004 (51.7μg/g in October) and the 

following winter/spring maximum in 2005 (85.3 μg/g in March) were the lowest seasonal 

concentrations observed since 1994. Concentrations of Cr and V declined from their maximum 

concentrations in the winter of 2002/2003 to concentrations similar to those prior to 2003. 

Copper concentrations in sediments are shown with sediment guidelines set by the 

National Oceanic and Atmospheric Administration (Long and others, 1995). Long and others 

defined values between ERL (Effects Range-Low) and ERM (Effects Range-Median) as 

concentrations that are occasionally associated with adverse effects (21 - 47% of the time for 

different metals). Values greater than the ERM were frequently associated with adverse effects 
11

(42% - 93% of the time for different metals). It must be remembered, however, that these effects 

levels were derived mostly from bioassay data and are not accurate estimates of sediment 

toxicity. In 2005, Cu concentrations were near or below the effects range-low (ERL) (34 μg/g) 

for the entire year, the first time this has been observed (Figure 6, Table 2). Cu concentrations 

were at their maximum (33-35 μg/g) throughout the winter/spring (January to April). The 

minimum concentration (21 μg/g) was observed in September. The magnitude of the interannual cycle was smaller than in some other years (e.g. 2004). Near-total Cu concentrations 

appear to have been declining gradually since at least 2000. Over the same period, partialextractable concentrations have remained relatively constant outside of the typical seasonal 

variation (Figure 6). 

For the second consecutive year, near-total and partial-extractable Zn concentrations 

never rose above the Zn ERL (150 μg/g) (Figure 7, Table 2). Winter Zn concentrations were the 

lowest observed during the past three years and were consistent with temporal patterns of Cu and 

Ni over the same period. 

The concentration of partial-extractable Ag in Palo Alto sediments are well below the Ag 

ERL (1 μg/g), but greater than the established concentration for uncontaminated sediments in 

San Francisco Bay (Hornberger and others, 1999) (Figure 8, Table 2). A seasonal pattern in Ag 

concentrations was well defined in 2005, but no long-term trend in this seasonal pattern is 

evident in the decade prior to 2005. 

Mercury concentrations in sediment during 2005 ranged between 0.26 μg/g (September) 

to 0.32 μg/g (January to April) (Figure 9, Table 2). These values were more typical of 

concentrations observed during the record (1994-2005) and were considerably less than the 

maximum Hg concentrations observed in 2004. The April 2004 concentration of Hg in the 

sediment (0.49 μg/g) was the highest observed in this study. Otherwise, Hg concentrations were 

within the range usually observed within San Francisco Bay (0.2 - 0.4 μg/g). 

Selenium concentrations were also less during 2005 than in 2004 (Figure 9, Table 2.) 

Concentrations ranged between 0.5 μg/g (February) to 0.3 μg/g (June and September). The 

annual mean concentration for the year was 0.38 ± 0.04 μg/g (Table 2), only slightly lower than 

the overall mean for the entire record (0.40 μg/g). 

Clam Tissue 

Metal concentrations in the soft tissues of Macoma petalum reflect the combined metal 

exposures from water and food. Exposures to Cu and Ag at Palo Alto are of special interest due 

to the high tissue concentrations observed at this site in the past relative to other South Bay 

locations (Figure 10 and Figure 11, Table 3 and Table 4, respectively). During the period 1977 

– 1987, the range in annual concentrations of Cu and Ag were 95-287 and 45-106 μg/g, 

respectively. Since 1987, concentrations have been considerably lower: 24-71 μg Cu /g and 2-20 

μg Ag/g. Annual mean concentrations of Cu and Ag for 2005 were, respectively, 26 ± 2 and 1.8 

± 0.3 μg/g, the lowest concentrations (Cu concentrations were comparable in 1991) observed 

during the record. 

Intra-annual variations in metal concentrations in clam soft tissues display a consistent 

seasonal signal, with fall/winter maxima and spring/summer minima, although it is common for 

the amplitude of this seasonal cycle to vary from year to year. For example, the winter maxima 

and the magnitude of seasonal Cu and Ag concentrations were greater between 1994 and 1996 

than in subsequent years (Figure 12, Figure13). The magnitude of the decline in Cu and Ag 

concentrations during the spring/summer of 2005 was comparable to previous years; however, 

the subsequent increase in tissue concentrations was not as great as in previous years and as of 
12

December, concentrations were only about half the maximum values observed in 2004. These 

trends most likely reflect the interaction of the changing exposure regime of the site (the long 

term decline in metal concentrations) with the annual growth cycle of M. petalum (Cain and 

Luoma 1990). 

As with Cu and Ag, tissue concentrations of Cr (Figure 14, Table 5), Ni (Figure 15, 

Table 5) and Zn (Figure 16, Table 5) also exhibited seasonal cycles. The seasonal cycles of Cr 

and Ni were very similar in terms of their timing and magnitude throughout the record (1994 - 

2005). Neither element exhibited a clear temporal trend (either decreasing or increasing) in 

concentration. Maximum concentrations occurred in the winter of 1996-1997, while 2000 – 

2002 was a period of relatively low winter-maximum concentrations. In 2003, concentrations 

increased somewhat and have remained relatively comparable through 2005. In addition to the 

typical seasonal pattern, Zn concentrations exhibited a slight long-term decline in concentration. 

During 1994-1997, Zn concentrations were notably higher throughout the year when compared 

to subsequent years. The winter maximum for 2004-05 was somewhat less than the previous two 

winters, but was comparable to the winter of 2001-02. Wellise and others (1999) observed that 

seasonal and inter-annual patterns of Cr, Ni, and Zn in M. petalum at Palo Alto were generally 

similar to those from the San Jose site, suggesting that regional-scale processes may be more 

important than treatment plant inputs in controlling the bioavailability of these elements. 

Mercury concentrations in M. petalum, like Zn, have trended slightly lower since 1994 

(Figure 17). The highest concentrations observed during the record occurred in September 1994 

(0.53 μg/g) and during the winters of 1995 (0.48 μg/g) and 1996 (0.47 μg/g). The seasonal 

(summer/fall) low concentration in 1995 (0.33 – 0.37 μg/g) was the highest recorded, also. 

Concentrations declined after 1996, and since then they have fluctuated seasonally between 0.12 

and 0.42 μg/g and averaged 0.26 ± 0.08 μg/g. 

Selenium concentrations in M. petalum vary seasonally like other elements (Figure 18, 

Table 5). Long-term trends in the data are not evident. However, the annual maximum 

concentrations (during summer/fall) have increased somewhat since 2002. Concentrations in 

2005 appear consistent with this more recent feature. 

The condition index for M. petalum at Palo Alto extends back to 1988 (Figure 19). As 

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

and annual cycles differ in magnitude. For example, the maximum value in the CI during 1994-

1999 was generally less than preceding or succeeding years. The CI during 2005 was generally 

comparable to the previous five years. 

Reproduction of Macoma petalum 

Earlier studies (Hornberger and others 2000b; Shouse and others 2004) found that low 

reproductive activity in M. petalum in the late 1970s was related to highly elevated 

concentrations of silver in the soft tissues. This finding has implications for the reproductive 

success of the population. Following the decline in tissue concentrations of Ag (and Cu) in the 

1980s, reproductive activity improved (Figure 20) . Furthermore, the low reproductive activity 

observed during the late 1970s has not been observed during the entire period of reduced metal 

exposures. Data for 2005 show that M. petalum continues to be highly reproductive relative to 

the 1970’s with a high percentage of the animals being reproductively active at any one time and 

with normal seasonal cycling of reproduction beginning in fall and spawning occurring during 

the following spring (see Appendix G for detailed reproduction data for 2005). 
13

Benthic Community 

The simplest metrics that are used in assessing environmental stress on biological 

communities are estimates of species diversity and total animal abundance. Species diversity, as 

estimated by a time series of number of species for each month, trended upward in 2005 (Figure 

22). However, total animal abundance does not show the same trend (Figure 23). The difficulty 

with these types of metrics is that they do not consider the possibility that one species can take 

the place of another. Depending on the characteristics of the new species, the community 

structure and function may change as a result of this exchange of species. 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. 

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

show any consistent trend over the 29-year period (Figure 24, Figure 25, and Figure 26). In all 

cases, there was significant seasonal and inter-annual variability in species abundances. There 

were, however, six species that did show trends in their abundance throughout the study. The 

first, Ampelisca abdita, a small crustacean that lives above the surface of the mudflat in a tube 

built from selected sediment particles showed a general decline in both the annual average 

abundances and annual maximum abundances (seasonal peaks in abundance; Figure 27). The 

second species to showed a significant trend was the small polychaete worm Streblospio 

benedicti, which also builds a tube above the surface of the mudflat. As with A. abdita, S. 

benedicti exhibited a decline in annual maximum abundances as well as annual average 

abundances (Figure 28). The small burrowing crustacean Grandiderella japonica, a deposit 

feeder, initially showed a declining trend through the 1980’s followed by increasing seasonal 

maximum abundances in recent years (Figure 29). Neanthes succinea, a burrowing polychaete 

that feeds on surface deposits and scavenges, similarly showed an initial decrease in annual 

maximum abundances through the 1980’s, followed by an increase in both annual average 

abundances and annual maximum abundances (Figure 30). Two species showed an increase in 

abundance within the time series. The first was the polychaete worm Heteromastus filiformis 

(Figure 31), a 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 partially 

receded in the late 1980’s. Abundances since 2000 have remained higher than in the late 1970’s. 

The second was an introduced species, Nippoleucon hinumensis, a small burrowing crustacean, 

which appeared in the dataset in 1988 (Figure 32) was introduced into the bay in 1986 (Cohen 

and Carlton 1995). Corbula amurensis, a non-indigenous filter feeding bivalve, first appeared in 

the benthic community as more than a rare species in April 2005 and persisted into November 

2005 (Appendix H). 

As stated earlier, multivariate analyses of population data of the dominant species with 

environmental parameters did not reveal any relationships, except with the concentration of 

silver and copper in the sediment and in the tissue of Macoma petalum (using data as reported by 

David and others 2002). Therefore, this update will only consider those metals (recent data, 

2002 through 2003, taken from Moon and others 2004). This comparison can be made by 

plotting the metals and individual species together over the period of the study. The worm H. 

filiformis has increased in abundance with the decrease in silver and copper through time (Figure 

33). Because the natural spatial variability (that is, the large standard deviations around the 

monthly means) and seasonal variability of invertebrate abundance and metal concentration can 

be quite large, the annual average abundances for H. filiformis and annual average metal 

concentrations are shown (Figure 34) and (Figure 35). To interpret these plots, we must first 
14

examine the life history characteristics of this species and determine if there is some mechanism 

by which this organism could be responding to a decrease in silver or copper in the environment. 

H. filiformis has continual tissue contact with the sediment both at the exterior of its body, as 

well as within its body, due to its lifestyle of burrowing through the sediment and consuming a 

diet of mud and organic particles. In addition, this is one of the few species in the present 

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

two to three days and spend two to three days in the plankton before settling back to the mud as 

juvenile worms (Rasmussen 1956). One hypothesis as to why H. filiformis increased in 

abundance may be that either the adult worms or the eggs are less stressed in the present 

environment. Because of its mode of reproduction and short planktonic larval period, this 

species is not likely to move into an area quickly after the environment becomes acceptable. 

Therefore, it is not possible to identify either the identity of the metal or the threshold 

concentration of the metal to which the animal is responding without laboratory tests. However, 

other investigators have shown that silver can adversely affect reproduction in invertebrates and 

that adult H. filiformis can tolerate high levels of copper (Ahn and others1995). The gradual 

increase in H. filiformis abundance through 1984 may be a response to the gradual reduction of 

metals in the environment or may indicate that it took several years for the population to build up 

in the area. The large abundance increase in 1985 and 1986, followed by a decline and leveling 

out of abundance, may be an example of the “boom and bust” principle whereby a species rises 

to levels too high for the habitat to support, and then declines in abundance until it levels out to a 

habitat-supportable abundance (Begon and others 1986). It is unclear, based on only eight years 

of data since the early 1990’s, if this species has established a stable abundance. 

The two species that have declined in abundance coincident with the decline in metals, 

the crustacean A. abdita (Figure 36, Figure 37 and Figure 38) and the worm S. benedicti (Figure 

39, Figure 40, and Figure 41) have very similar life history characteristics. Both species live on 

the surface of the sediment in tubes that are built from sediment particles, are known as 

opportunistic and are thus capable of rapid increase in population size and distribution, brood 

their young, and produce young that are capable of either swimming or settling upon hatching. It 

is unclear why these species have become less competitive in the present day environment, but 

their very low numbers in the last several years indicate that there is a major shift in the 

community as both species were numerically very dominant in the benthic community in the 

1970’s and 1980’s. Unlike A. abdita and S. benedicti, there has been no significant decline in the 

abundance of G. gemma (Figure 42, Figure 43, and Figure 44) the small clam that reproduces 

by brooding their young and lives on the sediment surface. All three species are suspension 

feeders and thus consume water borne particles, although S. benedicti may also deposit feed. 

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 updated 

previous findings (Luoma and others 1991; 1992; 1993; 1995; 1996; 1997; 1998; Wellise and 

others 1999; David and others 2002; Moon and others 2003; 2004; 2005, Shouse and others 

2003; 2004; Thompson and others 2002) with additional data from January 2005 through 

December 2005, to create a record spanning 32 years. This long-term dataset includes sediment 
15

chemistry, tissue concentrations of metals, condition index and reproductive activity in Macoma 

petalum, and population dynamics of benthic-invertebrate species. The time series encompasses 

the period when exceptionally high concentrations of copper and silver were found in M. 

petalum (1970’s) and the subsequent period when those concentrations declined. The sustained 

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

response to metal contamination within this ecosystem. 

Studies during the 1970’s showed that sediments and Macoma petalum at the Palo Alto 

site contained highly elevated levels of metals, especially Ag and Cu, as a result of metalcontaining effluent being discharged from the PARWQCP to South Bay. In the early 1980’s, the 

point-source metal loading from the nearby Palo Alto Regional Water Quality Control Plant 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). Hornberger and others found a significant 

correlation between metal loadings (Cu) and tissue concentrations in M. petalum. They also 

showed that metal levels in sediments and clams respond 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. 

Biological responses to metal inputs to South 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 (i.e. reproductive activity, a manifestation of a cellular or physiological change) 

to metal exposure may occur within a relatively short time, while 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 intraannual variability of benthic-community dynamics, which reflects the cumulative response to 

natural and anthropogenic disturbances. It is therefore critical that sampling frequency and 

duration be conducted at temporal scales appropriate to characterize the different biological 

responses. 

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

declining, the benthic community was composed of non-indigenous, opportunistic species that 

dominated due to their ability to survive the many physical disturbances on the mudflat (Nichols 

and Thompson 1985a, 1985b). These disturbances included sediment erosion and deposition, 

and aerial exposure at extreme low tides, in addition to less well defined stresses. The possible 

effects of metal exposure as a disturbance factor were not considered in the analyses by Nichols 

and Thompson as the decline in metal concentrations in Macoma petalum and sediment had just 

begun. 

However, data collected throughout the period of declining metal exposure have revealed 

biological responses. Reproductive activity improved within a year or two of reduced metal 

exposure, and responses at the population and community levels were observed afterward. 

Identification of these responses was possible because the frequency of sampling allowed longterm trends related to metal contamination to be identified within the context of repeating 

seasonal cycles and unrelated inter-annual variation. 
16

2005 

In 2005, Cu and Ag concentrations in sediments and the soft tissues of clam M. petalum

were as low as anytime during the record (that is, since 1974). This is at least partly attributable 

to the reduced loading of these metals from the treatment plant which was achieved in the 1990s 

and has been maintained thereafter. For many other elements of regulatory interest, including 

Cr, V, Ni, and Zn, regional scale factors appeared to influence sedimentary and bioavailable 

concentrations. Other variables such as precipitation and accelerated erosion of salt marsh banks 

in recent years, that may influence the seasonal and year to year patterns in sedimentary and 

tissue concentrations, should still be investigated. 

The long-term dataset demonstrates various adverse impacts 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 the clam Macoma petalum that has been sustained though 2005. The abundances of individual 

species showed little variability during 2005. This reflects a more stable community in the 

absence of metal stressors. All dominant species in the community, with the exception of 

Gemma gemma, have abundances similar to those seen in previous years. The lower abundances 

exhibited by G. gemma in 2004 were found elsewhere in the long-term data set, and could be due 

to a number interdependent factors. The interpretation that shifts in species abundance at Palo 

Alto were a response to decreasing contaminants continue to be supported by the most recent 

sediment and community data. 

Value of Long-Term Monitoring 

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

time series produced during the course of sustained efforts at this site have made it possible to 

describe trends, identify previously undocumented phenomena, and pose otherwise unrecognized 

hypotheses that have guided past detailed explanatory studies and can guide future studies. 

Monitoring studies cannot always unambiguously determine the causes of trends in metal 

concentrations or benthic-community structure. The strength and uniqueness of this study is the 

integrated analysis of metal exposure and biological response at intra- and inter-annual time 

scales over multiple decades. Changes and trends in community structure that may be related to 

anthropogenic stressors, as was seen in this study, can only be established with a concerted and 

committed effort of sufficient duration and frequency of sampling. Such rare field designs allow 

biological responses to natural stressors to be characterized and separated from those introduced 

by man. Through interpreting time series data, it has been possible to separate anthropogenic 

effects from natural annual and inter-annual variability. The data from the recent record (that is, 

within the past decade) increasingly appear to be indicative of an integrated regional ecological 

baseline with indicators of metal contamination, and greater physiological well-being of aquatic 

life and benthic-community structure. Changes are occurring in the South Bay watershed. For 

example, implementation is beginning in the South Bay Salt Ponds Restoration Program; with 

unknown implications (positive or negative) for all of South Bay. Nannotechnologies, many of 

which include metal-based products in forms for which we have no experience, are beginning to 

take hold in consumer products. The long-term, detailed, integrated ecological baseline that has 

been established at this sampling site will be uniquely valuable in assessing the response of the 

South Bay environment as our dynamic activities in the watershed continue to change. 
17

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Hornberger, M. I., Luoma, S. N., Van Geen, A., Fuller, C. C., and Anima, R., 1999, Historical 

trends of metals in the sediments of San Francisco Bay, California: Marine Chemistry, v. 64, 

p. 39-55. 
18

Hornberger, M. I., Luoma, S. N., Cain, D., Parchaso, F., Brown, C., Bouse, R., Wellise, C. J., 

Thompson, J., 2000a, Bioaccumulation of metals by the bivalve Macoma balthica at a site in 

South San Francisco Bay between 1977 and 1997: Long-term trends and associated biological 

effects with changing pollutant loadings: U. S. Geological Survey Open File Report 99-55, 42 

p.

Hornberger, M., Luoma, S., Cain, D., Parchaso, F., Brown, C., Bouse, R., Wellise, C., 

Thompson, J., 2000b, Linkage of bioaccumulation and biological effects to changes in 

pollutant loads in South San Francisco Bay: Environmental Science and Technology, v. 34, p. 

2401-2409. 

Kennish, J. K., 1998, Pollution impacts on marine biotic communities: CRC Press, New York. 

310 p. 

Long, E. R., MacDonald, D. D., Smith, S. L., and Calder, F. D., 1995, Incidence of adverse 

biological effects within ranges of chemical concentrations in marine and estuarine sediments: 

Environmental Management, v. 19, p. 81-97. 

Luoma, S. N., Cain, D. J., and Johansson, C., 1985, Temporal fluctuations of silver, copper and 

zinc in the bivalve Macoma balthica at five stations in South San Francisco Bay: 

Hydrobiologia, v. 129, p. 109-120.

Luoma, S. N., Cain, D. J., Brown, C. and Axtmann, E. V., 1991, Trace metals in clams (Macoma 

balthica) and sediments at the Palo Alto Mudflat in South San Francisco Bay: April, 1990 - 

April, 1991: U. S. Geological Survey Open File Report 91-460, 47p. 

Luoma, S. N., Cain, D. J., Brown, C. and Hornberger, M., 1992, Trace metals in clams (Macoma 

balthica) and sediments at the Palo Alto Mudflat in South San Francisco Bay: May 1991 - 

May 1992: U. S. Geological Survey Open File Report 92-456, 51p. 

Luoma, S. N., Cain, D. J., Brown, C. and Hornberger, M., 1993, Trace metals in clams (Macoma 

balthica) and sediments at the Palo Alto Mudflat in South San Francisco Bay: June 1992 - 

June 1993: U. S. Geological Survey Open File Report 93-500, 52p. 

Luoma, S. N., Cain, D. J., Brown, C. and Hornberger, M., 1995, Near field receiving water 

monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto and 

San Jose/Sunnyvale Water Quality Control Plants in South San Francisco Bay: June 1993 - 

October 1994: U. S. Geological Survey Open File Report 95-299, 83p. 

Luoma, S. N., Cain, D. J., Brown, C., Hornberger, M., and Bouse, R. 1996, Near field receiving 

water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto 

and San Jose/Sunnyvale Water Quality Control Plants in South San Francisco Bay: December 

1994 - December 1995: U. S. Geological Survey Open File Report 96-203, 90p. 

Luoma, S. N., Cain, D. J., Brown, C., Hornberger, M., and Bouse, R. 1997, Near field receiving 

water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto 
19

and San Jose/Sunnyvale Water Quality Control Plants in South San Francisco Bay: 1996: U. S. 

Geological Survey Open File Report 97-585, 91p. 

Luoma, S. N., Ho, Y.B, and. Bryan, G. W., 1995, Fate, bioavailability and toxicity of silver in 

estuarine environments: Marine Pollution Bulletin, v. 31, p. 44-54. 

Luoma, S. N., Wellise, C, Cain, D. J., Brown, C., Hornberger, M., and Bouse, R., 1998, Near 

field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments 

near the Palo Alto and San Jose/Sunnyvale Water Quality Control Plants in South San 

Francisco Bay: 1997: U. S. Geological Survey Open File Report 98-563, 88p. 

Morrisey, D.J., Underwood, A. J., and Howitt, L., 1996, Effects of copper on the faunas of 

marine soft-sediments: an experimental field study: Marine Biology, v. 125, p.199-213. 

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Near field receiving water monitoring of trace metals in clams (Macoma balthica) and 

sediments near the Palo Alto Water Quality Control Plant in South San Francisco Bay, 

California: 2002: U.S. Geological Survey Open File Report 03-339, 78p. 

Moon, E., Luoma, S. N, Cain, D. J, Hornberger, M. and David, C. P. C., 2004, Near field 

receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the 

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Nichols, F. N. and Thompson, J. K., 1985b, Time scales of change in the San Francisco Bay 

benthos: Hydrobiologia, v. 129, p. 121-138. 

Parchaso, F., 1993, Seasonal reproduction of Potamocorbula amurensis in San Francisco Bay, 

California: M.S. Thesis, San Francisco State University, San Francisco, CA. 

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Rygg, B., 1985, Effect of sediment copper on benthic fauna: Mar. Ecol. Prog. Ser., v. 25, p. 83-

89. 

SFEI (San Francisco Estuary Institute), 1997, RMP, Regional Monitoring Program for Trace 

Substances: 1996: Richmond, CA, 349 p. 

Shouse, M. K., 2002, The effects of decreasing trace metal concentrations on benthic community 

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of benthic community near the Palo Alto Water Quality Control Plant in South San Francisco 
20

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benthic community near the Palo Alto Water Quality Control Plant in South San Francisco 

Bay: February 1974 through December 2003. U.S. Geological Survey Open File Report 

2004-1210, Menlo Park, California, 39pp. 

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sediments and organisms in identifying sources of biologically available trace metal 

contamination: Water Research, v. 18, p. 755-765. 

Thompson, J. K., Parchaso, F., and Shouse, M. K., 2002, Near field receiving water monitoring 

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Francisco Bay: A potential for natural sources to dominate: Bull. Environ. Toxicol. Chem. v. 

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and Quantitation Approaches, EPA-821-B-04-005, U.S. Environmental Protection Agency, 

1200 Pennsylvania Avenue, NW Washington, DC 20460, 254p. 

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invertebrates: Sci. Total Environ., v. 237, p. 459-472. 

Wellise, C., Luoma, S. N., Cain, D. J., Brown, C., Hornberger, M., and Bouse, R., 1999, Near 

field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments 

near the Palo Alto and San Jose/Sunnyvale Water Quality Control Plants in South San 

Francisco Bay: 1998: U.S. Geological Survey Open File Report 99-455, 101pp. 
21

Figures 
22

-

Palo Alto

sampling site

1 Mile

Palo Alto

Sampling Site

Mudflats

Mudflats

sewage discharge

Yacht Harbor

Mayfield Slough

San Jose

Sampling Site

South Bay

Suisun Bay

Central

Bay

San Pablo

Bay

San

Francisco

Oakland

38 00'

37 30'

122 30'

Figure 1. Location of the Palo Alto sampling site in South San Francisco Bay. 

The intertidal zone is shaded light blue, subtidal in dark blue, and shoreline in brown. Effluent 

from the Palo Alto Regional Water Quality Control Plant is discharged approximately 1 mile 

north/west of the sampling site. The San Jose sampling site (inactive) also is shown for 

reference. 
23

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

Monthly Precipitation

0

2

4

6

8

10

12

14

Figure 2. Precipitation 

Data from San Mateo gauge station is for period from 1994 through 2005. Precipitation is in 

inches. 
24

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

Salinity (parts per thousand)

0

5

10

15

20

25

30

35

Figure 3. Water column salinity 

Data from Palo Alto site is for period from 1994 through 2005. 
25

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

0.0

2.5

5.0

7.5

10.0

12.5

0

20

40

60

80

100

Aluminum & Iron (percent dry weight)

Percent <100um

Figure 4. Aluminum, iron and silt/clay in sediments 

Data are for the period from 1994 through 2005. Percent aluminum (S), iron () and silt/clay 

(z) extracted by near-total digest. Data for percent fines for 2004 contain unquantifiable biases 

due to errors in sample processing, and therefore have been censored. Data for 2004 are shown 

in Appendices A-2 and A-3 for qualitative purposes only. 
26

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

0

50

100

150

200

Cr, V, and Ni in sediment (

μg/g)

Figure 5. Chromium, nickel and vanadium in sediments 

Data are for the period from 1994 through 2005. Concentrations of chromium (Cr) (), nickel 

(Ni) (z) and vanadium (V) (S) extracted by near-total digest. 
27

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

Cu in sediment (

μg/g)

0

20

40

60

80

260

280

300

ERM=270 μg/g

ERL=34 μg/g

Figure 6. Copper in sediments 

Data are for the period from 1994 through 2005. Near-total (S) and partial-extractable (|) 

copper. 
28

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

Zn in sediment (

μg/g)

0

50

100

150

200

400

450

500

ERM = 410 μg/g

ERL = 150 μg/g

Regional 

Background = 75 μg/g

Figure 7. Zinc in sediments 

Data are for the period from 1994 through 2005. Near-total (z) and partial-extractable (|) zinc. 
29

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

Ag in sediment (

μg/g)

0.0

0.2

0.4

0.6

0.8

1.0

3.0

3.5

4.0

ERM = 3.7 μg/g

ERL = 1 μg/g

Regional 

Background =

0.09 μg/g

Figure 8. Silver in sediments 

Data are for the period from 1994 through 2005. Data represent partial-extractable silver 

(treatment with 0.6 N hydrochloric acid). 
30

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

0.0

0.2

0.4

0.6

0.8

1.0

Se & in sediment (

μg/g) Hg 

Figure 9. Selenium and mercury in sediments 

Data are for the period from 1994 through 2005. Selenium (T); mercury (). 
31

Year

1970 1975 1980 1985 1990 1995 2000 2005

Cu in clam tissue (

μg/g)

0

100

200

300

400

Figure 10. Annual mean copper in Macoma petalum

The period of record is from 1977 through 2005. The error bars are the standard error of the 

mean (SEM). 
32

Year

1970 1975 1980 1985 1990 1995 2000 2005

Ag in clam tissue (

μg/g)

0

50

100

150

Figure 11. Annual mean silver in Macoma petalum

The period of record is from 1977 through 2005. The error bars are the standard error of the 

mean (SEM). 
33

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

Cu in clam tissue (

μg/g)

0

30

60

90

120

150

Figure 12. Copper in Macoma petalum

Each value is the mean concentration for the sample collected on a given date. The error bar is 

the standard error of the mean (SEM). 
34

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

Ag in clam tissue (

μg/g)

0

3

6

9

12

15

Figure 13. Silver in Macoma petalum

Each value is the mean concentration for the sample collected on a given date. The error bar is 

the standard error of the mean (SEM). 
35

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

0

3

6

9

12

Cr in clam tissue (

μg/g)

Figure 14. Chromium in Macoma petalum 

Each value is the mean concentration for the sample collected on a given date. The error bar is 

the standard error of the mean (SEM). 
36

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

Ni in clam tissue (

μg/g)

0

3

6

9

12

Figure 15. Nickel in Macoma petalum

Each value is the mean concentration for the sample collected on a given date. The error bar is 

the standard error of the mean (SEM). 
37

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

Zn in clam tissue (

μg/g)

0

100

200

300

400

500

600

700

Figure 16. Zinc in Macoma petalum

Each value is the mean concentration for the sample collected on a given date. The error bar is 

the standard error of the mean (SEM). 
38

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

0.0

0.2

0.4

0.6

0.8

1.0

Hg in clam tissue (

μg/g)

Figure 17. Mercury in Macoma petalum

Each value is the mean concentration for the sample collected on a given date. The error bar is 

the standard error of the mean (SEM). 
39

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

0

2

4

6

8

10

Se in clam tissue (

μg/g)

Figure 18. Selenium in Macoma petalum

Each value is the mean concentration for the sample collected on a given date. The error bar is 

the standard error of the mean (SEM). 
40

Date

1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

Tissue weight in mg (25mm clam)

0

50

100

150

200

250

300

Figure 19. Condition index of Macoma petalum

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

a shell length of 25 mm. 
41

Year

1975 1980 1985 1990 1995 2000 2005 

% Non-reproductive % Reproductive

-100

-50

0

50

100

Figure 20. Reproductive activity of Macoma petalum

Data are for the period from 1974 through 2005. 
42

Year

2000 2001 2002 2003 2004 2005 2006 

% Non-reproductive % Reproductive

-100

-50

0

50

100

Figure 21. Reproductive activity of Macoma petalum 2000 thru 2005 
43

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Species / 54cm2

0

10

20

30

Figure 22. Total number of species present 

Data are for the period from 1974 through 2005. 
44

Date

1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

500

1000

1500

Figure 23. Total average number of individuals present 

Data are for the period from 1974 through 2005. 
45

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

20

40

60

80

Figure 24. Average abundance of Macoma petalum

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
46

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

10

20

30

40

Figure 25. Average abundance of Mya arenaria

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
47

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

500

1000

1500

2000

Figure 26. Average abundance of Gemma gemma

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
48

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

250

500

750

Figure 27. Average abundance of Ampelisca abdita

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
49

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

150

300

450

600

Figure 28. Average abundance of Streblospio benedicti

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
50

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

20

40

60

80

100

Figure 29. Average abundance of Grandiderella japonica

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
51

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

5

10

15

Figure 30. Average abundance of Neanthes succinea 

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
52

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

20

40

60

80

Figure 31. Average abundance of Heteromastus filiformis

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
53

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

200

400

600

800

Figure 32. Average abundance of Nippoleucon hinumensis 

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. 
54

Number of Individuals / 54cm

2

0

20

40

60

80

Ag in clam tissue (

μg/g)

0

50

100

150

200

250

Date

1970 1975 1980 1985 1990 1995 2000 2005 

0

20

40

60

80

Cu in clam tissue (

μg/g)

0

100

200

300

400

500

600

Figure 33. Heteromastus filiformis abundance with silver and copper in Macoma 

petalum. 

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. The number of individuals (z); tissue concentration of silver () and 

copper ({) in M. petalum.
55

Ag in clam tissue (

μg/g)

0

50

100

150

Number of Individuals / 54cm2

0

10

20

30

40

50

60

Year

1970 1975 1980 1985 1990 1995 2000 2005

Ag in sediments (

μg/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 34. Heteromastus filiformis annual abundance with silver in M. petalum and 

sediment 

Data are for the period from 1974 through 2005. Error bars for abundance and metals in 

sediments are the standard deviation of the means. Error bars for metals in clams are the standard 

error of the mean (SEM). 
56

Cu in clam tissue (

μg/g)

0

100

200

300

400

Number of Individuals / 54cm2

0

10

20

30

40

50

60

Year

1970 1975 1980 1985 1990 1995 2000 2005

Cu in sediments (

μg/g)

0

30

60

90

120

Figure 35. Heteromastus filiformis annual abundance with copper in M. petalum and 

sediment 

Data are for the period from 1974 through 2004. Error bars for abundance and metals in 

sediments are the standard deviation of the means. Error bars for metals in clams are the standard 

error of the mean (SEM). 
57

0

250

500

750

Ag in clam tissue (

μg/g)

0

50

100

150

200

250

Date

1970 1975 1980 1985 1990 1995 2000 2005 

0

250

500

750

Cu in clam tissue (

μg/g)

0

100

200

300

400

500

600

Number of Individuals / 54cm

2

Figure 36. Ampelisca abdita abundance with silver and copper in M. petalum

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. Number of individuals (z) with silver () and copper ({) tissue 

concentrations in Macoma petalum.
58

Ag in clam tissue (

μg/g)

0

50

100

150

Number of Individuals / 54cm2

0

150

300

450

Year

1970 1975 1980 1985 1990 1995 2000 2005

Ag in sediments (

μg/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 37. Ampelisca abdita annual abundance with silver in M. petalum and sediment 

Data are for the period from 1974 through 2005. Error bars for abundance and metals in 

sediments are the standard deviation of the means. Error bars for metals in clams are the standard 

error of the mean (SEM). 
59

Cu in clam tissue (

μg/g)

0

100

200

300

400

Number of Individuals / 54cm2

0

150

300

450

Year

1970 1975 1980 1985 1990 1995 2000 2005

Cu in sediments (

μg/g)

0

30

60

90

120

Figure 38. Ampelisca abdita annual abundance with copper in M. petalum and sediment 

Data are for the period from 1974 through 2005. Error bars for abundance and metals in 

sediments are the standard deviation of the means. Error bars for metals in clams are the standard 

error of the mean (SEM). 
60

0

150

300

450

600

Ag in clam tissue (

μg/g)

0

50

100

150

200

250

Date

1970 1975 1980 1985 1990 1995 2000 2005 

0

150

300

450

600

Cu in clam tissue (

μg/g)

0

100

200

300

400

500

600

Number of Individuals / 54cm

2

Figure 39. Streblospio benedicti abundance with silver and copper in M. petalum 

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. Number of individuals (z) with silver () and copper ({) tissue 

concentrations in Macoma petalum.
61

Ag in clam tissue (

μg/g)

0

50

100

150

Number of Individuals / 54cm2

0

100

200

300

400

500

Year

1970 1975 1980 1985 1990 1995 2000 2005

Ag in sediments (

μg/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 40. Streblospio benedicti annual abundance with silver in M. petalum and 

sediment. 

Data are for the period from 1974 through 2005. Error bars for abundance and metals in 

sediments are the standard deviation of the means. Error bars for metals in clams are the standard 

error of the mean (SEM). 
62

Cu in clam tissue (

μg/g)

0

100

200

300

400

Number of Individuals / 54cm2

0

100

200

300

400

500

Year

1970 1975 1980 1985 1990 1995 2000 2005

Cu in sediments (

μg/g)

0

30

60

90

120

Figure 41. Streblospio benedicti annual abundance with copper in M. petalum and 

sediment 

Data are for the period from 1974 through 2005. Error bars for abundance and metals in 

sediments are the standard deviation of the means. Error bars for metals in clams are the standard 

error of the mean (SEM). 
63

0

500

1000

1500

2000

Ag in clam tissue (

μg/g)

0

50

100

150

200

250

Date

1970 1975 1980 1985 1990 1995 2000 2005 

0

500

1000

1500

2000

Cu in clam tissue (

μg/g)

0

100

200

300

400

500

600

Number of Individuals / 54cm

2

Figure 42. Gemma gemma abundance with silver and copper in M. petalum 

Data are for the period from 1974 through 2005. Error bars represent standard deviation from 3 

replicate samplings. Number of individuals (z) with silver () and copper ({) tissue 

concentrations in Macoma petalum.
64

Ag in clam tissue (

μg/g)

0

50

100

150

Number of Individuals / 54cm2

0

200

400

600

800

1000

Year

1970 1975 1980 1985 1990 1995 2000 2005

Ag in sediments (

μg/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 43. Gemma gemma annual abundance with silver in M. petalum and sediment. 

Data are for the period from 1974 through 2005. Error bars for abundance and metals in 

sediments are the standard deviation of the means. Error bars for metals in clams are the standard 

error of the mean (SEM). 
65

Cu in clam tissue (

μg/g)

0

100

200

300

400

Number of Individuals / 54cm2

0

200

400

600

800

1000

Year

1970 1975 1980 1985 1990 1995 2000 2005

Cu in sediments (

μg/g)

0

30

60

90

120

Figure 44. Gemma gemma annual abundance with copper in M. petalum and sediment 

Data are for the period from 1974 through 2005. Error bars for abundance and metals in 

sediments are the standard deviation of the means. Error bars for metals in clams are the standard 

error of the mean (SEM). 
66

Tables 
67

Table 1. Sediment characteristics and salinity in 2005 

Composition of sediment and salinity of water pooled on the sediment surface. Units for Al, Fe, total 

organic carbon (TOC) and sand are percent of dry weight. Sand is operationally determined as ≥ 100 μm 

grain size. Salinity is reported in units of parts per thousand (ppt). Data for Al and Fe are reported as the 

mean ± 1 standard deviation (std) for replicate subsamples (n=2); results for other constituents are for a 

single (n=1) measurement. Means for monthly samples were summarized and reported as the annual 

mean ± the standard error (SEM) (n=9). 

TOC Sand Salinity 

Date of sample (percent) (percent) (ppt)

mean std mean std

January 18, 2005 5.8 0.04 4.1 0.09 1.48 54 20

February 15, 2005 5.6 0.09 4.0 0.04 1.44 69 20

March 7, 2005 5.8 0.16 4.2 0.00 1.46 76 19

April 25, 2005 5.5 0.06 4.0 0.04 1.46 5 16

May 25, 2005 4.5 0.02 3.4 0.03 1.07 8 19

June 28, 2005 4.3 0.00 3.2 0.02 0.96 24 23

September 20, 2005 3.2 0.28 2.9 0.15 0.88 54 26

November 1, 2005 3.3 0.00 3.0 0.06 0.89 50 26

December 13, 2005 4.3 0.12 3.6 0.02 1.23 21 24

Annual Mean: 1.21 40 21

SEM: 0.3 0.2 0.09 9 1

Al Fe

4.7 3.6

(percent) (percent)
68

Table 2. Concentrations of trace elements in sediments in 2005 

Elemental concentrations for the monthly samples are reported as the mean ± 1 standard deviation (std) 

for replicate subsamples (n=2). Units are micrograms per gram dry weight. Means are summarized as 

the annual mean (the average of monthly means) and the standard error of the monthly means (SEM) 

(n=9). All concentrations are based on near-total extracts, except for silver (Ag) which is based on partial 

extraction (See Methods). 

Date of sample Hg Se

mean STD mean STD mean STD mean mean STD mean mean STD mean STD

January 18, 2005 0.48 0.006 129 3.4 35 1.1 0.32 83 1.7 0.5 135 3.2 138 1.3

February 15, 2005 0.49 0.003 124 2.5 33 0.4 0.31 80 1.0 0.4 128 1.0 132 2.1

March 7, 2005 0.46 0.002 131 5.6 35 0.1 - 85 0.6 - 133 2.1 140 0.6

April 25, 2005 0.59 0.007 124 1.4 35 0.3 0.32 79 0.5 0.4 130 1.4 131 0.2

May 25, 2005 0.32 0.007 116 1.0 28 0.1 - 65 0.6 - 106 0.6 107 0.7

June 28, 2005 0.35 0.001 117 1.7 26 0.3 0.28 62 0.1 0.3 100 3.4 101 1.3

September 20, 2005 0.26 0.083 84 7.6 21 0.1 0.26 58 2.6 0.3 59 8.5 90 3.4

November 1, 2005 0.33 0.001 89 0.1 23 0.2 - 60 1.4 - 56 4.9 94 0.6

December 13, 2005 0.44 0.015 104 3.4 30 0.9 - 74 0.4 - 73 2.0 121 1.6

Annual Mean: 0.41 113 30 0.30 72 0.38 102 117

SEM: 0.04 6 2 0.01 4 0.04 11 7

Ag Cr Cu Ni V Zn
69

Table 3. Annual mean copper in Macoma petalum and sediments 1977 through 2005 

Values are the annual (grand) means for 7 to 12 separate samples per year and standard errors of those 

means. Samples were collected between January and December of each year. Units are microgram per 

gram dry weight of soft tissue for the clam (Macoma petalum) and microgram per gram dry weight for 

sediment. 

Year Sediment Clam Tissue

Partial Total

1977 28 ± 6 45 ± 13 130 ± 23

1978 42 ± 11 57 ± 13 187 ± 104

1979 55 ± 13 86 ± 18 248 ± 114

1980 47 ± 5 66 ± 9 287 ± 66

1981 48 ± 7 57 ± 22 206 ± 55

1982 35 ± 4 34 ± 24 168 ± 35

1983 22 ± 9 38 ± 21 191 ± 48

1984 26 ± 10 40 ± 16 159 ± 55

1985 27 ± 3 45 ± 7 138 ± 22

1986 24 ± 3 49 ± 9 114 ± 49

1987 21 ± 3 47 ± 6 95 ±25

1988 27 ± 3 53 ± 5 53 ±24

1989 23 ± 6 44 ± 13 35 ± 10

1990 23 ± 2 51 ± 4 35 ± 11

1991 25 ± 2 52 ± 5 24 ± 8

1992 27 ± 6 52 ± 5 46 ± 14

1993 21 ± 3 43 ± 7 60 ± 14

1994 19 ± 2 45 ± 4 59 ± 12

1995 19 ± 2 44 ± 5 61 ± 16

1996 19 ± 2 43 ± 4 71 ± 11

1997 18 ± 1 43 ± 3 32 ± 7 

1998 20 ± 1 46 ± 2 35 ± 4

1999 18 ± 1 44 ± 2 34 ± 2

2000 18 ± 1 39 ± 3 32 ± 3

2001 17 ± 1 35 ± 2 31 ± 3

2002 13 ± 1 38 ± 2 36 ± 4

2003 19 ± 4 34 ± 8 29 ± 16

2004 17 ± 4 34 ± 8 33 ± 11

2005 16 ± 2 30 ± 2 26 ± 2
70

sediment. Sediment was extracted with 0.6 N hydrochloric acid. 

Table 4. Annual mean silver in Macoma petalum and sediments 1977 through 2005 

Values are annual (grand) means for 7 to 12 separate samples per year and standard errors of those 

means. Samples were collected between January and December of each year. Units are microgram per 

gram dry weight of soft tissue for the clam (Macoma petalum) and microgram per gram dry weight for 

Sediment Clam

Year Partial Tissue

1977 0.65 ± 0.59 87 ± 21

1978 1.39 ± 0.35 106 ± 17

1979 1.62 ± 0.28 96 ± 29

1980 1.28 ± 0.38 105 ± 24

1981 1.41 ± 0.15 63 ± 18

1982 0.74 ± 0.21 45 ± 13

1983 0.56 ± 0.26 56 ± 11

1984 0.64 ± 0.20 57 ± 18

1985 0.78 ± 0.14 58 ± 6

1986 0.61 ± 0.14 50 ± 20

1987 ND 55 ± 18

1988 ND 20 ± 10

1989 ND 11 ± 4

1990 0.39 ± 0.09 7.7 ± 3.4

1991 0.25 ± 0.07 3.3± 2.0

1992 0.35 ± 0.11 5.9 ± 1.9

1993 0.36± 0.09 6.9 ± 3.2

1994 0.46 ± 0.07 5.4 ± 1.1

1995 0.27 ± 0.05 5.5 ± 1.2

1996 0.24 ± 0.06 7.5 ± 1.6

1997 0.34 ± 0.04 3.6 ± 1.0

1998 0.34 ± 0.04 3.3 ± 0.6

1999 0.22 ± 0.01 3.6 ± 0.3

2000 0.34 ± 0.02 3.0 ± 0.4

2001 0.43 ± 0.03 3.0 ± 0.4

2002 0.31 ± 0.02 3.0 ± 0.5

2003 0.49 ± 0.08 2.1 ± 1.5

2004 0.29 ± 0.06 2.4 ± 1.3

2005 0.41 ± 0.04 1.8 ± 0.3
71

Table 5. Concentrations of trace elements in Macoma petalum in 2005. 

Monthly data are the mean and standard error (*SEM) for replicate composites (n= 6-14). The monthly 

means are summarized as the grand annual mean (the average of monthly means) and the standard 

error (SEM) (n=9). Elemental concentrations are microgram per gram soft tissue dry weight. The 

condition index is the soft tissue weight in milligrams of a 25 mm shell length clam. 

Date of sample Ag Cr Cu Hg Ni Se Zn Condition Index

January 18, 2005 mean 3.1 3.9 41 0.39 6.3 5.9 299 96

*SEM 0.2 0.5 2 0.00 0.3 0.8 24

February 15. 2005 mean 2.7 3.9 31 5.4 269 121

*SEM 0.5 0.2 3 0.2 9

March 7, 2005 mean 2.0 4.7 29 5.8 286 109

*SEM 0.3 0.5 3 1.5 38

April 25, 2005 mean 0.7 2.2 19 0.15 3.8 4.7 209 174

*SEM 0.0 0.2 0 0.05 0.2 0.8 8

May 25, 2005 mean 1.2 1.3 29 3.6 220 192

*SEM 0.3 0.0 9 0.2 11

June 28, 2005 mean 1.2 1.3 23 0.12 4.0 4.2 219 160

*SEM 0.1 0.1 1 0.05 0.3 0.4 21

September 20, 2005 mean 1.2 2.0 20 0.29 4.3 5.5 181 156

*SEM 0.1 0.2 1 0.14 0.2 1.3 12

November 1, 2005 mean 1.8 7.0 22 4.9 224 108

*SEM 0.1 0.3 1 0.3 16

December 13, 2005 mean 2.2 4.7 24 6.7 307 103

*SEM 0.1 0.5 1 0.5 19

Annual Mean: 1.8 3.4 26 0.2 5.0 5.1 246 135

SEM: 0.3 0.6 2 0.1 0.4 0.4 15 12
72

Appendix A 

Sediment characteristics for samples collected between 1994 and 2005. Results are for 

percent fine-grained particles (silt and clay < 100 μM) (A-1, A-2), and percent organic carbon 

(A-3). Data for percent fines for 2004 contain unquantifiable biases due to errors in sample 

processing. These data are shown for qualitative purposes only. 
73

A-1. PALTO ALTO GRAIN SIZE DATA: <100 μM 

Year Date %<100um Year Date %<100um Year Date %<100um

1994 01/10/94 61 1999 01/15/99 89 2004 01/20/04 45 

 02/08/94 48 02/26/99 91 02/27/04 42 

 03/22/94 88 03/22/99 92 03/16/04 49 

 04/20/94 82 04/18/99 96 04/12/04 49 

 06/13/94 90 05/19/99 71 05/24/04 64 

 09/20/94 60 06/16/99 68 06/22/04 71 

 10/17/94 83 09/13/99 32 09/13/04 24 

 12/12/94 84 11/23/99 61 10/13/04 28 

1995 01/18/95 59 12/20/99 95 12/08/04 15 

 02/22/95 98 2000 01/18/00 87 2005 01/18/05 46 

 03/27/95 76 02/15/00 83 02/15/05 32 

 04/25/95 78 03/22/00 84 03/07/05 24 

 06/06/95 90 04/10/00 92 04/25/05 95 

 07/01/95 69 06/19/00 60 05/25/05 92 

 08/01/95 48 09/13/00 70 06/28/05 76 

 09/25/95 56 11/09/00 66 09/20/05 46 

 10/24/95 80 12/12/00 61 11/01/05 50 

 12/05/95 76 2001 01/09/01 59 12/13/05 79 

1996 01/17/96 85 02/05/01 68 

 02/13/96 96 03/05/01 71 

 03/13/96 98 04/10/01 88 

 04/10/96 86 05/08/01 79 

 06/18/96 79 06/12/01 61 

 09/26/96 84 09/18/01 41 

 12/09/96 70 10/15/01 61 

1997 01/08/97 75 12/11/01 84 

 02/19/97 92 2002 01/08/02 55 

 03/19/97 53 02/08/02 62 

 04/14/97 86 03/07/02 96 

 06/11/97 93 04/15/02 86 

 09/17/97 54 05/15/02 80 

 10/15/97 59 06/11/02 89 

 12/09/97 84 09/09/02 65 

1998 01/07/98 94 10/07/02 41 

 02/04/98 87 12/16/02 77 

 03/03/98 91 2003 01/14/03 95 

 04/13/98 81 02/24/03 53 

 06/15/98 67 03/25/03 79 

 09/09/98 78 04/22/03 50 

 10/20/98 74 05/05/03 48 

 12/14/98 71 06/04/03 56 

 09/11/03 25 

 10/09/03 39 

 12/18/03 48 
74

A-2. Percent of sediment composed of silt/clay-sized particles (< 100 uM)

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 

Percent silt/clay (< 100 uM)

20

40

60

80

100

120
75

A-3. Total organic carbon (TOC) content (expressed as percent) of sediment collected in 2005. 

Date of collection TOC (%) 

January 18, 2005 1.48 

February 15, 2005 1.44 

March 7, 2005 1.46 

April 25, 2005 1.46 

May25, 2005 1.07 

June 28, 2005 0.96 

September 20, 2005 0.88 

November 1, 2006 0.89 

December 13, 2005 1.23 
Appendix B 

Metal concentrations in sediments collected at the Palo Alto mudflat during 2005 and determined by ICP-OES. Replic

analyzed for each collection. The dry weight, reconstitution volume and dilution factor (if applicable) are shown for eaConcentrations are reported for sample solutions (in micrograms per milliliter, μg/ml) and the calculated weight standa(reported as microgram per gram dry sediment, μg/g). The sample mean and standard deviation for the weight standar

are reported, also. 

76
Palo Alto Total Extracts: 2005 

Concentration, μg/mL 

1/18/2005: 46% <100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.5643 10 5 649.7 1.429 0.404 452.5 12.14 0.9259 0.35

Tot2 0.4975 10 5 578.7 1.307 0.3402 411.5 10.9 0.8403 0.32

Concentration, μg/g 

57566.9 126.617 35.79656 40093.92 1075.669 82.0397 31.880

58160.8 131.3568 34.19095 41356.78 1095.477 84.45226 32.442

Tot1 Average 57863.85 128.9869 34.99376 40725.35 1085.573 83.24598 32.161

Tot2 Std 419.9557 3.3515 1.135336 892.9785 14.00667 1.705942 0.3973

Concentration, μg/mL 

2/15/2005: 32% < 100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.5275 10 5 583.6 1.286 0.3487 417.4 12.14 0.8365 0.33

Tot2 0.5069 10 5 573.1 1.272 0.3409 406.3 11.89 0.8188 0.3

Concentration, μg/g 

55317.54 121.8957 33.05213 39563.98 1150.711 79.2891 31.345

56529.89 125.4685 33.62596 40076.94 1172.815 80.76544 31.189

Tot1 Average 55923.71 123.6821 33.33905 39820.46 1161.763 80.02727 31.267

Tot2 Std 857.2623 2.526351 0.405758 362.7155 15.63007 1.043928 0.1105

77
Concentration, μg/mL 

3/07/2005: 24% <100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.5072 10 5 597.3 1.372 0.3584 422.3 11.44 0.8613 0.3Tot2 0.5041 10 5 571.4 1.284 0.357 419.7 11.46 0.8643 0.3

Concentration, μ /g g 

58882.1 135.2524 35.33123 41630.52 1127.76 84.90733 33.20

56675.26 127.3557 35.40964 41628.65 1136.679 85.72704 33.34

Tot1 Average 57778.68 131.304 35.37044 41629.58 1132.22 85.31719 33.27Tot2 Std 1560.468 5.583798 0.055445 1.326104 6.30667 0.579618 0.102

Concentration, μg/mL 

4/25/2005: 8895% <100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.2514 5 5 551.7 1.235 0.349 395.3 12.54 0.7948 0.3Tot2 0.234 5 5 521.8 1.168 0.3214 372.9 11.75 0.7464 0.2

Concentration, μ /g g 

54862.77 122.8123 34.70565 39309.86 1247.017 79.03739 30.4455747.86 124.7863 34.33761 39839.74 1255.342 79.74359 30.71

Tot1 Average 55305.32 123.7993 34.52163 39574.8 1251.179 79.39049 30.58Tot2 Std 625.8565 1.395881 0.260245 374.6809 5.886787 0.499358 0.188

78
Concentration, μg/mL 

5/025/2005: 92% < 100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.5134 10 5 461.2 1.194 0.2916 350 5.257 0.6704 0.2Tot2 0.549 10 5 489.3 1.262 0.3105 369 5.568 0.7071 0.2

Concentration, μ /g g 

44916.24 116.2836 28.39891 34086.48 511.979 65.29022 23.6544562.84 114.9362 28.27869 33606.56 507.1038 64.39891 23.84

Tot1 Average 44739.54 115.6099 28.3388 33846.52 509.5414 64.84456 23.74Tot2 Std 249.8937 0.952722 0.085009 339.3581 3.447244 0.630255 0.132

Concentration, μg/mL 

6/28/2005: 76% <100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.5602 10 5 487.3 1.327 0.2922 358.2 7.461 0.6903 0.2Tot2 0.5203 10 5 452.4 1.207 0.2667 336.3 7.009 0.6422 0.2

Concentration, μ /g g 

43493.4 118.4398 26.07997 31970.72 665.9229 61.61192 23.08

43474.92 115.9908 25.62944 32317.89 673.5537 61.7144 23.82

Tot1 Average 43484.16 117.2153 25.85471 32144.31 669.7383 61.66316 23.45Tot2 Std 13.06514 1.731753 0.318571 245.4854 5.395815 0.072458 0.518

79
Concentration, μg/mL 

9/20/2005: 46% <100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.4924 10 5 334.9 0.8838 0.2083 299.3 5.336 0.5895 0.2Tot2 0.5942 10 5 357.5 0.9389 0.2523 336.1 6.081 0.6679 0.2

Concentration, μ /g g 

34006.9 89.74411 21.1515 30391.96 541.8359 59.85987 22.73

30082.46 79.00539 21.23023 28281.72 511.6964 56.20162 21.32

Tot1 Average 32044.68 84.37475 21.19086 29336.84 526.7662 58.03074 22.02Tot2 Std 2774.999 7.593425 0.055665 1492.161 21.31185 2.586776 0.998

Concentration, μg/mL 

11/01/2005: 50% <100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.51 10 5 333.9 0.9049 0.2309 311.4 6.074 0.6211 0.2Tot2 0.5646 10 5 369.4 1 0.253 334.8 6.484 0.6653 0.2

Concentration, μ /g g 

32735.29 88.71569 22.63725 30529.41 595.4902 60.89216 23.7832713.43 88.55827 22.40524 29649.31 574.2118 58.91782 22.89

Tot1 Average 32724.36 88.63698 22.52125 30089.36 584.851 59.90499 23.33Tot2 Std 15.46349 0.111309 0.164057 622.3265 15.04608 1.396068 0.63

80
Concentration, μg/mL 

12/13/052001: 79% <100 μm 

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.55 10 5 465.5 1.123 0.3247 389.6 9.034 0.8111 0.Tot2 0.5483 10 5 482.6 1.172 0.3376 392 9.026 0.8148 0.3

Concentration, μ /g g 

42318.18 102.0909 29.51818 35418.18 821.2727 73.73636 27.6344008.75 106.8758 30.78607 35746.85 823.0895 74.30239 27.86

Tot1 Average 43163.47 104.4834 30.15212 35582.52 822.1811 74.01938 27.75Tot2 Std 1195.415 3.383427 0.89653 232.4063 1.284687 0.400241 0.16

81
Palo Alto HCl Extracts: 2005 

Concentration, μg/mL 

1/18/05: 46% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN NI 

HCl1 0.5123 12 0.0209 112.7 0.2179 0.7696 229.6 38.4 0.HCL2 0.5054 12 0.0201 107.5 0.2109 0.7381 220.3 37.58 0.

Concentration, μg/g 

0.4895569 2639.859 5.104041 18.026937 5378.099 899.473 7.64

0.47724575 2552.434 5.007519 17.525129 5230.708 892.2833 7.48

HCl1 Average 0.48340132 2596.147 5.05578 17.776033 5304.404 895.8782 7.56HCl2 Std 0.00615558 43.71287 0.048261 0.2509044 73.69521 3.594813 0.07

Concentration, μg/mL 

2/15/05: 32% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN NI 

HCl1 0.5057 12 0.0207 104.9 0.1974 0.6747 213.8 40.41 HCL2 0.4962 12 0.0206 103.6 0.196 0.6733 210.3 39.97 0.

Concentration, μg/g 

0.49120032 2489.223 4.6842 16.010283 5073.364 958.9084 7.11

0.49818622 2505.441 4.740024 16.28295 5085.852 966.6264 7.12

HCl1 Average 0.49469327 2497.332 4.712112 16.146617 5079.608 962.7674 7.12HCl2 Std 0.00349295 8.109247 0.027912 0.1363338 6.244412 3.858958 0.0

82
Concentration, μg/mL 

3/07/05: 24% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN N

HCl1 0.4988 12 0.0192 111.3 0.2226 0.6596 253.4 38.94 0HCL2 0.5056 12 0.0196 117.1 0.2441 0.6747 267.1 39.49 0.3

Concentration, μg/g 

0.46190858 2677.626 5.355253 15.868484 6096.231 936.8083 8.2030.46518987 2779.272 5.793513 16.013449 6339.399 937.2627 8.63

HCl1 Average 0.46354923 2728.449 5.574383 15.940967 6217.815 937.0355 8.417HCl2 Std 0.00164065 50.82292 0.21913 0.0724825 121.5839 0.227159 0.214

Concentration, μg/mL 

4/25/05: 95% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN N

HCl1 0.417 12 0.0209 86.21 0.1678 0.5763 173.9 36.88 0.2HCL2 0.4406 12 0.0216 93.26 0.1864 0.6196 190 39.07 0.2

Concentration, μg/g 

0.60143885 2480.863 4.828777 16.584173 5004.317 1061.295 7.648

0.5882887 2539.991 5.076714 16.87517 5174.762 1064.094 7.90

HCl1 Average 0.59486377 2510.427 4.952745 16.729671 5089.539 1062.695 7.774HCl2 Std 0.00657508 29.56381 0.123968 0.1454988 85.22257 1.399726 0.126

83
Concentration, μg/mL 

5/25/05: 92% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN N

HCl1 0.5128 12 0.0139 84.93 0.1713 0.6076 200.3 12.06 0.2HCL2 0.5364 12 0.0139 86.01 0.1739 0.6297 205.2 12.59 0

Concentration, μg/g 

0.32527301 1987.441 4.00858 14.218409 4687.207 282.2153 6.7020.31096197 1924.161 3.89038 14.087248 4590.604 281.6555 6.532

HCl1 Average 0.31811749 1955.801 3.94948 14.152829 4638.906 281.9354 6.617HCl2 Std 0.00715552 31.64021 0.0591 0.0655802 48.30173 0.279904 0.084

Concentration, μg/mL 

6/28/05: 76% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN N

HCl1 0.534 12 0.0154 83.57 0.1724 0.5798 200.6 20.98 0.2HCl2 0.5192 12 0.0149 82.14 0.1695 0.5669 197.9 20.58 0.2

Concentration, μg/g 

0.34606742 1877.978 3.874157 13.029213 4507.865 471.4607 5.973

0.34437596 1898.459 3.917565 13.102465 4573.96 475.6549 6.1

HCl1 Average 0.34522169 1888.218 3.895861 13.065839 4540.913 473.5578 6.04HCl2 Std 0.00084573 10.24082 0.021704 0.0366259 33.04738 2.09709 0.068

84
Concentration, μg/mL 

9/20/05: 46% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN N

HCl1 0.4969 12 0.0072 40.81 0.1781 0.5565 213.5 15.17 0HCl2 0.5158 12 0.0146 84.97 0.1857 0.5904 220.3 15.7 0.3

Concentration, μg/g 

0.17387804 985.5504 4.301067 13.439324 5155.967 366.3514 7.120.33966654 1976.813 4.320279 13.735556 5125.242 365.2579 7.200

HCl1 Average 0.25677229 1481.182 4.310673 13.58744 5140.605 365.8046 7.162HCl2 Std 0.08289425 495.6312 0.009606 0.1481163 15.36233 0.546763 0.038

Concentration, μg/mL 

11/01/05: 50% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN N

HCl1 0.4956 12 0.0138 84.38 0.1789 0.5915 217.4 17.69 0.3HCl2 0.5289 12 0.0146 90.51 0.1915 0.646 231 18.75 0.3

Concentration, μg/g 

0.33414044 2043.099 4.331719 14.322034 5263.923 428.3293 7.6730.33125355 2053.545 4.344867 14.656835 5241.066 425.4112 7.72

HCl1 Average 0.33269699 2048.322 4.338293 14.489434 5252.494 426.8703 7.697HCl2 Std 0.00144345 5.22291 0.006574 0.1674005 11.42808 1.459033 0.023

85
86

Concentration, μg/mL 

12/13/05: 79% < 100μm 

Sample Weight (g) Recon. (ml) AG AL CR CU FE MN N

HCl1 0.5432 12 0.0193 111.4 0.2397 0.8219 278 29.49 0.3HCl2 0.5212 12 0.0198 107.9 0.2293 0.7949 269.2 29.12 0.3

Concentration, μg/g 

0.4263623 2460.972 5.295287 18.156848 6141.384 651.4728 8.518

0.45587107 2484.267 5.279355 18.301612 6198.005 670.4528 8.502

HCl1 Average 0.44111668 2472.62 5.287321 18.22923 6169.694 660.9628 8.510HCl2 Std 0.01475438 11.64753 0.007966 0.0723817 28.31011 9.490024 0.007
87

Appendix C 

Metal concentrations in the clam Macoma petalum collected at the Palo Alto Mudflat. Each monthly 

collection is reported on two pages. The first page contains summary statistics: 

Mean concentrations in microgram per gram dry tissue weight (μg/g). 

• STD is the standard deviation of the mean. 

• SEM is the standard error of the mean. 

• CV percent is the coefficient of variation. 

• r wt x [] is the correlation coefficient for the concentration versus weight correlation for each 

element. 

• X 100mg is the concentration interpolated from the above regression for a 100 mg animal. 

• r l x [] is the correlation coefficient for the concentration versus shell length regression. 

• X 20 mm and X 25 mm are concentrations interpolated from the regression for 20mm and 25 

mm animals. 

Condition index (CI) is an estimate of the tissue dry weight (g or mg) standardized to a 

constant shell length (shell length of 25 mm is used for interpretive purposes). This index, along 

with weights for animals of 15 mm and 20 mm shell length, was estimated from a linear regression 

analysis of log tissue dry weight vs. log average shell length for each monthly collection. 

Content (a measure of metal bioaccumulation that is standardized to tissue mass) is show 

from 15 mm, 20 mm and 25 mm animals. 

The second page shows the analysis of each composite within the sample, the number of 

animals in each composite, concentration as calculated from sample dry weight and the dilution 

factor and the metal content for each composite. 
88

0

0

Station: Palo Alto Statistical Summary

Date: 1/18/05

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 3.0962 0.2065 3.8795 41.2623 6.3217 1.7580 4.4338 299.0293

STD 0.6493 0.0760 1.4413 5.5812 0.8578 0.6015 1.5460 66.923

SEM 0.230 0.027 0.510 1.973 0.303 0.213 0.547 23.661

CV% 20.972 36.800 37.151 13.526 13.569 34.212 34.868 22.38

n 88888888

r wt x [ ] 0.217 0.677 0.965 0.675 0.665 0.950 0.950 0.251

X 100mg 3.142 0.190 3.431 40.047 6.138 1.574 3.960 304.451

r l x [ ] 0.087 0.666 0.967 0.651 0.658 0.963 0.958 0.232

X 20mm 3.072 0.228 4.478 42.822 6.564 2.007 5.070 292.373

X 25mm 3.119 0.186 3.323 39.812 6.096 1.527 3.842 305.217

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.1615 0.0112 0.2157 2.2348 0.3429 0.0980 0.2468 15.4136

25mm 0.2904 0.0163 0.2915 3.7565 0.5740 0.1368 0.3415 28.2917

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.025 gm 0.053 gm

24.970 mg 53.189 mg

Estimated weight for 25mm clam

0.096 gm

95.618 mg
Station: Palo Alto Macoma petalum

Date: 1/18/05

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-AES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 13.89 0.1664 0.0185 10 0.0609 0.0044 0.0966 0.7041 0.1178 0.0435 0.1113 5.264

Mb2 15.32 0.2615 0.0327 10 0.0814 0.008 0.1483 1.289 0.1927 0.065 0.1643 6.88

Mb3 19.49 0.221 0.0442 10 0.0541 0.0047 0.1012 1.038 0.142 0.0474 0.1102 5.786

Mb4 21.07 0.2299 0.0575 10 0.0536 0.0039 0.0922 0.8977 0.1374 0.0392 0.1036 6.254

Mb5 26.17 0.3491 0.1164 10 0.1305 0.0059 0.0988 1.247 0.1849 0.0408 0.1122 11.58

Mb6 26.48 0.3143 0.1048 10 0.0961 0.0093 0.1184 1.393 0.2244 0.0522 0.1392 11.06

Mb7 28.77 0.2824 0.1412 10 0.0689 0.0029 0.0721 0.9249 0.1762 0.0333 0.0864 5.327

Mb8 29.53 0.3039 0.1520 10 0.121 0.004 0.0553 1.206 0.1534 0.0336 0.07 12.36

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 3.6599 0.2644 5.8053 42.3137 7.0793 2.6142 6.6887 316.346

Mb2 3.1128 0.3059 5.6711 49.2925 7.3690 2.4857 6.2830 263.098

Mb3 2.4480 0.2127 4.5792 46.9683 6.4253 2.1448 4.9864 261.810

Mb4 2.3314 0.1696 4.0104 39.0474 5.9765 1.7051 4.5063 272.031

Mb5 3.7382 0.1690 2.8301 35.7204 5.2965 1.1687 3.2140 331.710

Mb6 3.0576 0.2959 3.7671 44.3207 7.1397 1.6608 4.4289 351.893

Mb7 2.4398 0.1027 2.5531 32.7514 6.2394 1.1792 3.0595 188.633

Mb8 3.9816 0.1316 1.8197 39.6841 5.0477 1.1056 2.3034 406.713

Sample #

 Content (ug) ==> Mb1 0.0677 0.0049 0.1073 0.7823 0.1309 0.0483 0.1237 5.8489

Mb2 0.1018 0.0100 0.1854 1.6113 0.2409 0.0813 0.2054 8.6000

Mb3 0.1082 0.0094 0.2024 2.0760 0.2840 0.0948 0.2204 11.5720

Mb4 0.1340 0.0098 0.2305 2.2443 0.3435 0.0980 0.2590 15.6350

Mb5 0.4350 0.0197 0.3293 4.1567 0.6163 0.1360 0.3740 38.6000

Mb6 0.3203 0.0310 0.3947 4.6433 0.7480 0.1740 0.4640 36.8667

Mb7 0.3445 0.0145 0.3605 4.6245 0.8810 0.1665 0.4320 26.6350

Mb8 0.6050 0.0200 0.2765 6.0300 0.7670 0.1680 0.3500 61.8000

89
90

1

8

Station:Palo Alto Statistical Summary

Date: 2/15/05

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 2.7347 0.1386 3.8578 30.7929 5.3820 1.4474 4.3918 268.7910

STD 1.3224 0.0508 0.6857 9.1042 0.6971 0.3056 0.7353 26.847

SEM 0.468 0.018 0.242 3.219 0.246 0.108 0.260 9.492

CV% 48.358 36.672 17.773 29.566 12.952 21.114 16.743 9.98

n 88888888

r wt x [ ] 0.684 0.617 0.005 0.875 0.876 0.553 0.234 0.842

X 100mg 3.773 0.175 3.862 39.937 6.083 1.641 4.589 294.717

r l x [ ] 0.680 0.588 0.036 0.893 0.887 0.582 0.265 0.815

X 20mm 3.268 0.156 3.872 35.612 5.749 1.553 4.507 281.763

X 25mm 3.973 0.180 3.892 41.987 6.233 1.692 4.660 298.922

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.2001 0.0100 0.2509 2.3241 0.3806 0.1020 0.2945 18.5968

25mm 0.4263 0.0207 0.4636 4.9210 0.7482 0.2018 0.5568 35.8472

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.030 gm 0.066 gm

29.867 mg 65.793 mg

Estimated weight for 25mm clam

0.121 gm

121.401 mg
Station:Palo Alto Macoma petula

Date: 2/15/05

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-AES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 9.23 0.2287 0.0079 10 0.0554 0.0034 0.0878 0.5450 0.1117 0.0308 0.0952 6.2600

Mb2 10.17 0.1928 0.0101 10 0.0363 0.0019 0.0700 0.4522 0.0924 0.0215 0.0790 4.3660

Mb3 10.82 0.176 0.0117 10 0.0381 0.0013 0.0596 0.4638 0.0851 0.0214 0.0660 4.4890

Mb4 12.21 0.217 0.0181 10 0.0379 0.0023 0.0880 0.4604 0.0991 0.0283 0.0956 5.1850

Mb5 17.62 0.2217 0.0443 10 0.0483 0.0034 0.0958 0.7050 0.1269 0.0369 0.1090 5.9970

Mb6 21.70 0.2647 0.0882 10 0.0737 0.0058 0.1358 0.9524 0.1711 0.0546 0.1551 7.7600

Mb7 23.65 0.3268 0.1089 10 0.0926 0.0065 0.1209 1.1440 0.1966 0.0511 0.1453 9.8350

Mb8 24.37 0.2082 0.1041 10 0.1221 0.0023 0.0583 1.0140 0.1202 0.0272 0.0728 6.0700

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 2.4224 0.1487 3.8391 23.8303 4.8841 1.3467 4.1627 273.721

Mb2 1.8828 0.0985 3.6307 23.4544 4.7925 1.1151 4.0975 226.452

Mb3 2.1648 0.0739 3.3864 26.3523 4.8352 1.2159 3.7500 255.057

Mb4 1.7465 0.1060 4.0553 21.2166 4.5668 1.3041 4.4055 238.940

Mb5 2.1786 0.1534 4.3212 31.7997 5.7240 1.6644 4.9166 270.501

Mb6 2.7843 0.2191 5.1303 35.9804 6.4639 2.0627 5.8595 293.162

Mb7 2.8335 0.1989 3.6995 35.0061 6.0159 1.5636 4.4461 300.949

Mb8 5.8646 0.1105 2.8002 48.7032 5.7733 1.3064 3.4966 291.547

Sample #

 Content (ug) ==> Mb1 0.0191 0.0012 0.0303 0.1879 0.0385 0.0106 0.0328 2.1586

Mb2 0.0191 0.0010 0.0368 0.2380 0.0486 0.0113 0.0416 2.2979

Mb3 0.0254 0.0009 0.0397 0.3092 0.0567 0.0143 0.0440 2.9927

Mb4 0.0316 0.0019 0.0733 0.3837 0.0826 0.0236 0.0797 4.3208

Mb5 0.0966 0.0068 0.1916 1.4100 0.2538 0.0738 0.2180 11.9940

Mb6 0.2457 0.0193 0.4527 3.1747 0.5703 0.1820 0.5170 25.8667

Mb7 0.3087 0.0217 0.4030 3.8133 0.6553 0.1703 0.4843 32.7833

Mb8 0.6105 0.0115 0.2915 5.0700 0.6010 0.1360 0.3640 30.3500

91
Station: Palo Alto Statistical Summary

Date: 03/08/2005

Ag Cd Cr Cu Ni Pb V

Mean(ug/g) 1.9814 0.1941 4.7303 28.5787 5.8330 1.8242 5.2627

STD 0.7891 0.0676 1.3332 9.1795 1.5393 0.6386 1.6210

SEM 0.298 0.026 0.504 3.470 0.582 0.241 0.613

CV% 39.827 34.806 28.185 32.120 26.390 35.008 30.802

n 7777777

r wt x [ ] 0.872 0.522 0.461 0.873 0.588 0.539 0.513

X 100mg 2.674 0.230 5.349 36.637 6.744 2.171 6.100

r l x [ ] 0.897 0.583 0.587 0.928 0.704 0.669 0.639

X 20mm 2.283 0.211 5.064 32.210 6.295 2.006 5.704

X 25mm 2.852 0.243 5.692 39.056 7.166 2.349 6.536

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V

20mm 0.1406 0.0129 0.3170 2.0326 0.3969 0.1251 0.3568

25mm 0.2994 0.0252 0.6071 4.2158 0.7685 0.2506 0.6971

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.031 gm 0.063 gm

31.354 mg 63.159 mg

Estimated weight for 25mm clam

0.109 gm

108.732 mg

92
Station: Palo Alto Macoma petalum

Date: 03/08/2005

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-AES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 11.41 0.3139 0.0149 10 0.0501 0.0058 0.135 0.7364 0.162 0.0485 0.1442 7.489

Mb2 12.27 0.3278 0.0193 10 0.054 0.0052 0.1226 0.6959 0.1538 0.0421 0.1318 7.838

Mb3 12.98 0.3211 0.0229 10 0.048 0.0068 0.1518 0.7239 0.1742 0.0539 0.164 7.222

Mb4 14.15 0.2632 0.0292 10 0.0256 0.0023 0.0775 0.4895 0.1055 0.0289 0.0849 5.27

Mb5 19.72 0.1806 0.0602 10 0.0379 0.0034 0.1055 0.6276 0.1233 0.0438 0.1192 5.784

Mb6 23.89 0.1797 0.0899 10 0.0556 0.0056 0.1254 0.7335 0.1554 0.0522 0.1448 8.963

Mb7 27.01 0.2771 0.1386 10 0.0822 0.006 0.1269 1.071 0.1682 0.0508 0.145 7.767

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 1.5960 0.1848 4.3007 23.4597 5.1609 1.5451 4.5938 238.579

Mb2 1.6473 0.1586 3.7401 21.2294 4.6919 1.2843 4.0207 239.109

Mb3 1.4949 0.2118 4.7275 22.5444 5.4251 1.6786 5.1074 224.914

Mb4 0.9726 0.0874 2.9445 18.5980 4.0084 1.0980 3.2257 200.228

Mb5 2.0986 0.1883 5.8416 34.7508 6.8272 2.4252 6.6002 320.266

Mb6 3.0940 0.3116 6.9783 40.8180 8.6477 2.9048 8.0579 498.776

Mb7 2.9664 0.2165 4.5796 38.6503 6.0700 1.8333 5.2328 280.296

Sample #

 Content (ug) ==> Mb1 0.0239 0.0028 0.0643 0.3507 0.0771 0.0231 0.0687 3.5662

Mb2 0.0318 0.0031 0.0721 0.4094 0.0905 0.0248 0.0775 4.6106

Mb3 0.0343 0.0049 0.1084 0.5171 0.1244 0.0385 0.1171 5.1586

Mb4 0.0284 0.0026 0.0861 0.5439 0.1172 0.0321 0.0943 5.8556

Mb5 0.1263 0.0113 0.3517 2.0920 0.4110 0.1460 0.3973 19.2800

Mb6 0.2780 0.0280 0.6270 3.6675 0.7770 0.2610 0.7240 44.8150

Mb7 0.4110 0.0300 0.6345 5.3550 0.8410 0.2540 0.7250 38.8350

93
94

2

Station:Palo Alto Statistical Summary

Date: 4/25/05

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 0.7277 0.0677 2.1632 18.8436 3.8003 0.9253 2.3310 208.5782

STD 0.0914 0.0303 0.5777 1.2084 0.5238 0.2176 0.6893 25.094

SEM 0.030 0.011 0.193 0.403 0.175 0.073 0.230 8.365

CV% 12.556 44.764 26.706 6.413 13.782 23.517 29.569 12.031

n 98999999

r wt x [ ] 0.424 0.098 0.259 0.322 0.361 0.323 0.152 0.918

X 100mg 0.709 0.064 2.091 18.656 3.892 0.891 2.281 219.701

r l x [ ] 0.497 0.296 0.215 0.375 0.350 0.309 0.118 0.885

X 20mm 0.702 0.056 2.093 18.588 3.904 0.887 2.285 221.090

X 25mm 0.646 0.038 1.938 18.025 4.132 0.804 2.184 248.704

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.0629 0.0041 0.1833 1.6848 0.3552 0.0781 0.2000 20.1487

25mm 0.1118 0.0059 0.3278 3.1310 0.7153 0.1375 0.3684 42.6031

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.040 gm 0.091 gm

39.578 mg 91.131 mg

Estimated weight for 25mm clam

0.174 gm

174.028 mg
Station:Palo Alto Macoma petalum

Date: 4/25/05

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-OES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 13.47 0.6459 0.0323 20 0.028 0.0027 0.057 0.6332 0.1041 0.0272 0.0577 6.473

Mb2 14.31 0.6514 0.0326 20 0.0248 0.0026 0.0621 0.6189 0.1145 0.0294 0.0656 6.423

Mb3 15.39 0.5437 0.0418 20 0.021 0.0027 0.0797 0.5142 0.117 0.0327 0.0883 5.072

Mb4 15.88 0.5021 0.0456 20 0.0177 0.0023 0.0713 0.4963 0.1058 0.031 0.078 4.774

Mb5 16.77 0.5796 0.0580 20 0.0187 0.0016 0.051 0.5857 0.1077 0.0202 0.0556 5.719

Mb6 17.35 0.3203 0.0534 15 0.0147 0.0003 0.0384 0.3552 0.0721 0.0172 0.0374 4.617

Mb7 18.56 0.3554 0.0711 15 0.016 0.0008 0.0528 0.4673 0.0761 0.0202 0.0551 4.546

Mb8 21.54 0.4996 0.1249 20 0.0211 0.0021 0.0714 0.4307 0.1173 0.0286 0.0815 5.889

Mb9 26.35 0.2 0.2000 10 0.0118 0 0.0276 0.3698 0.0789 0.0129 0.0313 5.233

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 0.8670 0.0836 1.7650 19.6068 3.2234 0.8422 1.7867 200.434

Mb2 0.7614 0.0798 1.9067 19.0021 3.5155 0.9027 2.0141 197.206

Mb3 0.7725 0.0993 2.9318 18.9148 4.3038 1.2029 3.2481 186.573

Mb4 0.7050 0.0916 2.8401 19.7690 4.2143 1.2348 3.1070 190.161

Mb5 0.6453 0.0552 1.7598 20.2105 3.7164 0.6970 1.9186 197.343

Mb6 0.6884 0.0140 1.7983 16.6344 3.3765 0.8055 1.7515 216.219

Mb7 0.6753 0.0338 2.2285 19.7228 3.2119 0.8526 2.3255 191.868

Mb8 0.8447 0.0841 2.8583 17.2418 4.6958 1.1449 3.2626 235.749

Mb9 0.5900 1.3800 18.4900 3.9450 0.6450 1.5650 261.650

Sample #

 Content (ug) ==> Mb1 0.0280 0.0027 0.0570 0.6332 0.1041 0.0272 0.0577 6.4730

Mb2 0.0248 0.0026 0.0621 0.6189 0.1145 0.0294 0.0656 6.4230

Mb3 0.0323 0.0042 0.1226 0.7911 0.1800 0.0503 0.1358 7.8031

Mb4 0.0322 0.0042 0.1296 0.9024 0.1924 0.0564 0.1418 8.6800

Mb5 0.0374 0.0032 0.1020 1.1714 0.2154 0.0404 0.1112 11.4380

Mb6 0.0368 0.0008 0.0960 0.8880 0.1803 0.0430 0.0935 11.5425

Mb7 0.0480 0.0024 0.1584 1.4019 0.2283 0.0606 0.1653 13.6380

Mb8 0.1055 0.0105 0.3570 2.1535 0.5865 0.1430 0.4075 29.4450

Mb9 0.1180 0.2760 3.6980 0.7890 0.1290 0.3130 52.3300

95
96

4

Station:Palo Alto Statistical Summary

Date:5/25/05

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 1.1725 0.1464 1.2800 29.3699 3.6114 1.1597 1.5150 219.6712

STD 0.8368 0.0258 0.1442 25.9842 0.6253 0.1856 0.1953 33.4198

SEM 0.279 0.009 0.048 8.661 0.208 0.062 0.065 11.140

CV% 71.366 17.637 11.267 88.472 17.316 16.003 12.888 15.21

n 99999999

r wt x [ ] 0.167 0.317 0.263 0.338 0.703 0.709 0.460 0.313

X 100mg 1.206 0.148 1.289 31.481 3.717 1.128 1.537 222.184

r l x [ ] 0.242 0.365 0.214 0.429 0.591 0.673 0.430 0.335

X 20mm 1.239 0.149 1.290 33.025 3.733 1.119 1.543 223.339

X 25mm 1.492 0.161 1.329 46.965 4.195 0.963 1.648 237.329

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.0872 0.0131 0.1135 2.3010 0.3275 0.0962 0.1358 19.5746

25mm 0.1826 0.0299 0.2517 5.9251 0.7816 0.1827 0.3108 44.4160

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.033 gm 0.089 gm

32.566 mg 88.507 mg

Estimated weight for 25mm clam

0.192 gm

192.208 mg
Station:Palo Alto Macoma petalum

Date:5/25/05

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-OES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 14.67 0.2799 0.0280 15 0.0268 0.0028 0.0257 0.4277 0.0658 0.0233 0.0305 3.84

Mb2 15.37 0.3675 0.0408 15 0.0309 0.0034 0.0298 0.635 0.0794 0.0341 0.0326 5.766

Mb3 15.83 0.375 0.0417 20 0.018 0.0027 0.0215 0.4087 0.0684 0.0231 0.0274 3.82

Mb4 16.35 0.3096 0.0387 15 0.0159 0.0031 0.0286 0.4026 0.0763 0.027 0.0321 4.983

Mb5 16.98 0.3577 0.0511 15 0.0199 0.0032 0.0336 0.5413 0.0697 0.0254 0.0372 4.826

Mb6 18.84 0.3972 0.0662 20 0.0142 0.0025 0.0212 0.3063 0.0602 0.0211 0.0232 4.237

Mb7 20.08 0.2908 0.0969 15 0.0171 0.0024 0.0215 0.4501 0.0781 0.0218 0.0279 3.173

Mb8 24.20 0.3206 0.1603 15 0.0697 0.0045 0.0307 2.094 0.0727 0.0266 0.0394 6.088

Mb9 25.89 0.2289 0.2289 10 0.0099 0.0032 0.0314 0.3405 0.1146 0.0174 0.0376 5.185

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 1.4362 0.1501 1.3773 22.9207 3.5263 1.2487 1.6345 205.788

Mb2 1.2612 0.1388 1.2163 25.9184 3.2408 1.3918 1.3306 235.347

Mb3 0.9600 0.1440 1.1467 21.7973 3.6480 1.2320 1.4613 203.733

Mb4 0.7703 0.1502 1.3857 19.5058 3.6967 1.3081 1.5552 241.424

Mb5 0.8345 0.1342 1.4090 22.6992 2.9228 1.0651 1.5600 202.376

Mb6 0.7150 0.1259 1.0675 15.4230 3.0312 1.0624 1.1682 213.343

Mb7 0.8820 0.1238 1.1090 23.2170 4.0285 1.1245 1.4391 163.669

Mb8 3.2611 0.2105 1.4364 97.9726 3.4014 1.2445 1.8434 284.841

Mb9 0.4325 0.1398 1.3718 14.8755 5.0066 0.7602 1.6426 226.518

Sample #

 Content (ug) ==> Mb1 0.0402 0.0042 0.0386 0.6416 0.0987 0.0350 0.0458 5.7600

Mb2 0.0515 0.0057 0.0497 1.0583 0.1323 0.0568 0.0543 9.6100

Mb3 0.0400 0.0060 0.0478 0.9082 0.1520 0.0513 0.0609 8.4889

Mb4 0.0298 0.0058 0.0536 0.7549 0.1431 0.0506 0.0602 9.3431

Mb5 0.0426 0.0069 0.0720 1.1599 0.1494 0.0544 0.0797 10.3414

Mb6 0.0473 0.0083 0.0707 1.0210 0.2007 0.0703 0.0773 14.1233

Mb7 0.0855 0.0120 0.1075 2.2505 0.3905 0.1090 0.1395 15.8650

Mb8 0.5228 0.0338 0.2303 15.7050 0.5453 0.1995 0.2955 45.6600

Mb9 0.0990 0.0320 0.3140 3.4050 1.1460 0.1740 0.3760 51.8500

97
98

0

Station:Palo Alto Statistical Summary

Date:6/28/05

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 1.2074 0.1553 1.2463 23.1143 3.9771 0.9418 1.4605 219.1300

STD 0.1650 0.0288 0.2872 3.2238 0.8804 0.2405 0.3106 65.8869

SEM 0.052 0.009 0.091 1.019 0.278 0.076 0.098 20.835

CV% 13.664 18.572 23.047 13.947 22.136 25.533 21.270 30.067

n 10 10 10 10 10 10 10 1

r wt x [ ] 0.197 0.499 0.618 0.546 0.150 0.554 0.449 0.292

X 100mg 1.225 0.147 1.151 22.165 4.049 0.870 1.385 229.499

r l x [ ] 0.104 0.466 0.505 0.439 0.221 0.477 0.332 0.216

X 20mm 1.211 0.152 1.212 22.784 4.023 0.915 1.436 222.445

X 25mm 1.236 0.132 1.000 20.708 4.308 0.747 1.285 243.281

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.0903 0.0112 0.0878 1.6887 0.2987 0.0657 0.1052 16.1324

25mm 0.1953 0.0209 0.1577 3.3066 0.6827 0.1157 0.2037 36.2024

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.028 gm 0.075 gm

28.433 mg 75.186 mg

Estimated weight for 25mm clam

0.160 gm

159.848 mg
Station:Palo Alto Macoma petalum

Date:6/28/05

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-OES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 15.06 0.2925 0.0293 15 0.0252 0.0032 0.0264 0.4749 0.0764 0.0191 0.0294 4.206

Mb2 15.80 0.3236 0.0360 15 0.0273 0.0033 0.023 0.4884 0.0742 0.019 0.0239 4.394

Mb3 16.89 0.3306 0.0413 15 0.0249 0.0033 0.0275 0.5479 0.0683 0.0203 0.0313 4.035

Mb4 17.38 0.3215 0.0459 15 0.0185 0.0036 0.0291 0.4333 0.0736 0.0223 0.0334 4.188

Mb5 18.15 0.292 0.0487 15 0.0261 0.0031 0.0272 0.4471 0.0756 0.0185 0.0324 3.738

Mb6 18.82 0.3022 0.0604 15 0.0268 0.003 0.0272 0.4888 0.0707 0.0208 0.0318 3.787

Mb7 19.80 0.2662 0.0666 15 0.0217 0.0039 0.0324 0.5206 0.1102 0.0261 0.037 6.199

Mb8 20.51 0.2888 0.0963 15 0.0205 0.0028 0.0222 0.4777 0.0875 0.017 0.0289 3.3

Mb9 24.11 0.3403 0.1702 15 0.0325 0.0032 0.0203 0.4113 0.0916 0.0165 0.0264 7.524

Mb10 25.51 0.2902 0.1451 15 0.0219 0.002 0.0158 0.3786 0.0715 0.0103 0.0197 3.117

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 1.2923 0.1641 1.3538 24.3538 3.9179 0.9795 1.5077 215.692

Mb2 1.2655 0.1530 1.0661 22.6391 3.4394 0.8807 1.1078 203.677

Mb3 1.1298 0.1497 1.2477 24.8593 3.0989 0.9211 1.4201 183.076

Mb4 0.8631 0.1680 1.3577 20.2162 3.4339 1.0404 1.5583 195.397

Mb5 1.3408 0.1592 1.3973 22.9675 3.8836 0.9503 1.6644 192.021

Mb6 1.3302 0.1489 1.3501 24.2621 3.5093 1.0324 1.5784 187.972

Mb7 1.2228 0.2198 1.8257 29.3351 6.2096 1.4707 2.0849 349.305

Mb8 1.0648 0.1454 1.1530 24.8113 4.5447 0.8830 1.5010 171.399

Mb9 1.4326 0.1411 0.8948 18.1296 4.0376 0.7273 1.1637 331.649

Mb10 1.1320 0.1034 0.8167 19.5693 3.6957 0.5324 1.0183 161.113

Sample #

 Content (ug) ==> Mb1 0.0378 0.0048 0.0396 0.7124 0.1146 0.0287 0.0441 6.3090

Mb2 0.0455 0.0055 0.0383 0.8140 0.1237 0.0317 0.0398 7.3233

Mb3 0.0467 0.0062 0.0516 1.0273 0.1281 0.0381 0.0587 7.5656

Mb4 0.0396 0.0077 0.0624 0.9285 0.1577 0.0478 0.0716 8.9743

Mb5 0.0653 0.0078 0.0680 1.1178 0.1890 0.0463 0.0810 9.3450

Mb6 0.0804 0.0090 0.0816 1.4664 0.2121 0.0624 0.0954 11.3610

Mb7 0.0814 0.0146 0.1215 1.9523 0.4133 0.0979 0.1388 23.2463

Mb8 0.1025 0.0140 0.1110 2.3885 0.4375 0.0850 0.1445 16.5000

Mb9 0.2438 0.0240 0.1523 3.0848 0.6870 0.1238 0.1980 56.4300

Mb10 0.1643 0.0150 0.1185 2.8395 0.5363 0.0773 0.1478 23.3775

99
Station:Palo Alto Statistical Summary

Date: 9/20/2005

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 1.1749 0.0830 1.9802 20.0444 4.2462 1.2504 2.1876 181.4699

STD 0.2309 0.0641 0.5426 1.8523 0.6627 0.2934 0.6419 35.1094

SEM 0.082 0.024 0.192 0.655 0.234 0.104 0.227 12.413

CV% 19.650 77.241 27.401 9.241 15.606 23.463 29.343 19.347

n 87888888

r wt x [ ] 0.515 0.502 0.634 0.258 0.928 0.648 0.764 0.661

X 100mg 1.005 0.003 1.489 19.362 3.369 0.979 1.488 148.377

r l x [ ] 0.634 0.583 0.639 0.322 0.933 0.634 0.784 0.735

X 20mm 1.071 0.039 1.735 19.623 3.809 1.119 1.832 163.204

X 25mm 0.851 -0.031 1.213 18.724 2.876 0.838 1.073 124.283

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.0752 0.0034 0.1185 1.3964 0.2690 0.0772 0.1237 11.5122

25mm 0.1409 0.0046 0.2054 2.9261 0.4906 0.1387 0.1989 21.1850

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.026 gm 0.072 gm

26.265 mg 71.665 mg

Estimated weight for 25mm clam

0.156 gm

156.112 mg

100
Station:Palo Alto Macoma petalum

Date: 9/20/2005

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-OES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 13.44 0.1483 0.0185 10 0.0211 0.0033 0.0317 0.3360 0.0716 0.0187 0.0389 3.1710

Mb2 14.04 0.1646 0.0206 10 0.0242 0.0010 0.0394 0.3551 0.0829 0.0244 0.0456 3.7850

Mb3 15.33 0.1826 0.0261 10 0.0237 0.0008 0.0371 0.3400 0.0821 0.0235 0.0408 4.0880

Mb4 17.29 0.2509 0.0418 10 0.0220 0.0022 0.0706 0.5180 0.1186 0.0402 0.0724 3.6480

Mb5 18.21 0.3515 0.0586 15 0.0250 0.0018 0.0502 0.3880 0.0967 0.0345 0.0578 3.7400

Mb6 19.63 0.358 0.0716 15 0.0312 0.0013 0.0431 0.4692 0.0982 0.0301 0.0480 3.5150

Mb7 20.13 0.3423 0.0685 15 0.0204 0.0008 0.0245 0.4628 0.0801 0.0181 0.0266 3.7740

Mb8 23.15 0.2322 0.1161 10 0.0247 0.0001 0.0335 0.4728 0.0727 0.0196 0.0312 3.8650

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 1.4228 0.2225 2.1376 22.6568 4.8281 1.2610 2.6231 213.823

Mb2 1.4702 0.0608 2.3937 21.5735 5.0365 1.4824 2.7704 229.951

Mb3 1.2979 0.0438 2.0318 18.6199 4.4962 1.2870 2.2344 223.877

Mb4 0.8768 0.0877 2.8139 20.6457 4.7270 1.6022 2.8856 145.397

Mb5 1.0669 0.0768 2.1422 16.5576 4.1266 1.4723 2.4666 159.602

Mb6 1.3073 0.0545 1.8059 19.6592 4.1145 1.2612 2.0112 147.277

Mb7 0.8940 0.0351 1.0736 20.2805 3.5101 0.7932 1.1656 165.381

Mb8 1.0637 1.4427 20.3618 3.1309 0.8441 1.3437 166.451

Sample #

 Content (ug) ==> Mb1 0.0264 0.0041 0.0396 0.4200 0.0895 0.0234 0.0486 3.9638

Mb2 0.0303 0.0013 0.0493 0.4439 0.1036 0.0305 0.0570 4.7313

Mb3 0.0339 0.0011 0.0530 0.4857 0.1173 0.0336 0.0583 5.8400

Mb4 0.0367 0.0037 0.1177 0.8633 0.1977 0.0670 0.1207 6.0800

Mb5 0.0625 0.0045 0.1255 0.9700 0.2418 0.0863 0.1445 9.3500

Mb6 0.0936 0.0039 0.1293 1.4076 0.2946 0.0903 0.1440 10.5450

Mb7 0.0612 0.0024 0.0735 1.3884 0.2403 0.0543 0.0798 11.3220

Mb8 0.1235 0.1675 2.3640 0.3635 0.0980 0.1560 19.3250

101
Station:Palo Alto Statistical Summary

Date:11/01/05

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 1.7569 0.0774 3.5709 22.1437 4.9075 1.6865 3.5419 224.2923

STD 0.3617 0.0382 1.1811 3.8988 1.0686 0.4127 1.1688 55.4973

SEM 0.104 0.011 0.341 1.125 0.308 0.119 0.337 16.021

CV% 20.587 49.395 33.076 17.607 21.776 24.469 32.998 24.743

n 12 9 12 12 12 12 12 12

r wt x [ ] 0.083 0.209 0.688 0.559 0.788 0.761 0.792 0.550

X 100mg 1.675 0.054 1.348 28.110 2.601 0.826 1.008 140.761

r l x [ ] 0.188 0.261 0.648 0.506 0.774 0.704 0.781 0.600

X 20mm 1.696 0.068 2.885 23.909 4.167 1.426 2.724 194.466

X 25mm 1.612 0.054 1.932 26.360 3.139 1.065 1.588 153.041

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.0931 0.0032 0.1520 1.3076 0.2278 0.0782 0.1448 10.6068

25mm 0.1747 0.0054 0.2398 2.7128 0.3781 0.1302 0.2197 17.9956

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.024 gm 0.056 gm

23.771 mg 55.723 mg

Estimated weight for 25mm clam

0.108 gm

107.902 mg

102
Station:Palo Alto Macoma petalum

Date:11/01/05

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-OES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 10.17 0.0583 0.0083 10 0.0149 -0.0017 0.0232 0.1194 0.0341 0.0094 0.0266 2.016

Mb2 11.59 0.141 0.0108 10 0.0223 0.0016 0.059 0.2801 0.0825 0.0295 0.07 3.315

Mb3 12.46 0.1353 0.0123 10 0.0262 0.0012 0.0534 0.2983 0.0767 0.0284 0.0547 3.647

Mb4 13.58 0.1436 0.0180 10 0.018 0.0013 0.0824 0.2676 0.0865 0.0324 0.0628 3.008

Mb5 14.59 0.1093 0.0219 10 0.0171 -0.0004 0.0443 0.2195 0.0573 0.0215 0.0457 2.524

Mb6 15.46 0.1175 0.0235 10 0.0168 0.0004 0.0514 0.2261 0.0656 0.0237 0.0562 3.058

Mb7 17.15 0.2462 0.0352 10 0.0478 0.0023 0.0862 0.5368 0.1135 0.0373 0.0714 4.142

Mb8 18.39 0.2448 0.0490 10 0.0433 0.0005 0.0371 0.5416 0.0726 0.0251 0.0386 2.994

Mb9 19.54 0.3323 0.0554 15 0.0488 0.0031 0.0941 0.7065 0.1231 0.0398 0.0885 4.696

Mb10 20.25 0.2274 0.0569 10 0.0327 0.0012 0.0547 0.4368 0.097 0.0318 0.0529 5.423

Mb11 21.27 0.205 0.0683 10 0.0352 0.0013 0.0609 0.5666 0.0845 0.0281 0.0594 3.848

Mb12 22.35 0.1453 0.0727 10 0.0246 -0.0009 0.0281 0.3299 0.0458 0.0158 0.0276 3.076

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 2.5557 <MDL 3.9794 20.4803 5.8491 1.6123 4.5626 345.798

Mb2 1.5816 0.1135 4.1844 19.8652 5.8511 2.0922 4.9645 235.106

Mb3 1.9364 0.0887 3.9468 22.0473 5.6689 2.0990 4.0429 269.549

Mb4 1.2535 0.0905 5.7382 18.6351 6.0237 2.2563 4.3733 209.471

Mb5 1.5645 <MDL 4.0531 20.0823 5.2425 1.9671 4.1812 230.924

Mb6 1.4298 0.0340 4.3745 19.2426 5.5830 2.0170 4.7830 260.255

Mb7 1.9415 0.0934 3.5012 21.8034 4.6101 1.5150 2.9001 168.237

Mb8 1.7688 0.0204 1.5155 22.1242 2.9657 1.0253 1.5768 122.304

Mb9 2.2028 0.1399 4.2477 31.8914 5.5567 1.7966 3.9949 211.977

Mb10 1.4380 0.0528 2.4055 19.2084 4.2656 1.3984 2.3263 238.478

Mb11 1.7171 0.0634 2.9707 27.6390 4.1220 1.3707 2.8976 187.707

Mb12 1.6930 <MDL 1.9339 22.7047 3.1521 1.0874 1.8995 211.700

Sample #

 Content (ug) ==> Mb1 0.0213 <MDL 0.0331 0.1706 0.0487 0.0134 0.0380 2.8800

Mb2 0.0172 0.0012 0.0454 0.2155 0.0635 0.0227 0.0538 2.5500

Mb3 0.0238 0.0011 0.0485 0.2712 0.0697 0.0258 0.0497 3.3155

Mb4 0.0225 0.0016 0.1030 0.3345 0.1081 0.0405 0.0785 3.7600

Mb5 0.0342 <MDL 0.0886 0.4390 0.1146 0.0430 0.0914 5.0480

Mb6 0.0336 0.0008 0.1028 0.4522 0.1312 0.0474 0.1124 6.1160

Mb7 0.0683 0.0033 0.1231 0.7669 0.1621 0.0533 0.1020 5.9171

Mb8 0.0866 0.0010 0.0742 1.0832 0.1452 0.0502 0.0772 5.9880

Mb9 0.1220 0.0078 0.2353 1.7663 0.3078 0.0995 0.2213 11.7400

Mb10 0.0818 0.0030 0.1368 1.0920 0.2425 0.0795 0.1323 13.5575

Mb11 0.1173 0.0043 0.2030 1.8887 0.2817 0.0937 0.1980 12.8267

Mb12 0.1230 <MDL 0.1405 1.6495 0.2290 0.0790 0.1380 15.3800

103
Station:Palo Alto Statistical Summary

Date:12/13/05

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 2.1763 0.1472 4.6964 23.9117 6.6689 1.9373 5.4205 306.7428

STD 0.4357 0.0559 1.7196 3.0080 1.7119 0.5177 2.1549 66.0008

SEM 0.131 0.017 0.518 0.907 0.516 0.156 0.650 19.900

CV% 20.021 37.966 36.616 12.579 25.669 26.725 39.754 21.517

n 11 6 11 11 11 11 11 11

r wt x [ ] 0.079 0.012 0.741 0.539 0.795 0.696 0.726 0.608

X 100mg 2.283 0.145 0.752 18.891 2.457 0.822 0.580 182.531

r l x [ ] 0.074 0.149 0.782 0.451 0.786 0.639 0.764 0.561

X 20mm 2.213 0.139 3.176 22.376 5.147 1.563 3.557 264.876

X 25mm 2.251 0.125 1.578 20.763 3.549 1.170 1.599 220.889

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.1139 0.0077 0.1635 1.1907 0.2721 0.0817 0.1816 14.0053

25mm 0.2200 0.0168 0.2454 2.2057 0.4445 0.1368 0.2674 24.6473

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.023 gm 0.053 gm

22.752 mg 53.190 mg

Estimated weight for 25mm clam

0.103 gm

102.776 mg

104
Station:Palo Alto Macoma petalum

Date:12/13/05

Average Total Average Recon Concentration (ug/ml) - Blank Corrected from ICP-OES

Sample #-n Length (mm) Dry Wt (gm) Dry Wt (gm) Amt (ml) Ag Cd Cr Cu Ni Pb V Zn

Mb1 9.19 0.0363 0.0061 10 0.0078 -0.0017 0.0246 0.0796 0.0303 0.0081 0.0298 0.9678

Mb2 10.56 0.0476 0.0095 10 0.0092 -0.001 0.0359 0.1223 0.0422 0.0117 0.0412 1.486

Mb3 11.52 0.0862 0.0096 10 0.0195 -0.0002 0.034 0.2084 0.0549 0.0149 0.0409 3.52

Mb4 12.48 0.1276 0.0116 10 0.026 0.0023 0.0641 0.3566 0.0995 0.0298 0.0772 4.953

Mb5 13.48 0.0968 0.0161 10 0.0248 0 0.0462 0.2537 0.0621 0.0175 0.0491 3.147

Mb6 14.64 0.1715 0.0172 10 0.0368 0.0034 0.0911 0.4344 0.1239 0.0378 0.0954 5.644

Mb7 16.05 0.0722 0.0241 10 0.015 0.0003 0.0439 0.1814 0.0637 0.0204 0.0567 2.45

Mb8 18.38 0.2795 0.0466 10 0.057 0.0043 0.0873 0.6268 0.1446 0.0412 0.089 6.842

Mb9 19.63 0.2442 0.0611 10 0.0395 0.0042 0.0977 0.4657 0.1361 0.0413 0.11 7.764

Mb10 20.39 0.2476 0.0619 10 0.0811 0.0034 0.0873 0.6529 0.1294 0.0371 0.1003 6.654

Mb11 21.34 0.1174 0.0587 10 0.0216 -0.0015 0.0183 0.2202 0.0416 0.0124 0.0204 2.041

MDL 0.0011 0.0002 0.0073 0.0021 0.0016 0.0036 0.0018 0.0054

MRL 0.0021 0.0003 0.0146 0.0043 0.0032 0.0072 0.0036 0.0108

Sample #

 Concentration (ug/g) ==> Mb1 2.1488 <MDL 6.7769 21.9284 8.3471 2.2314 8.2094 266.612

Mb2 1.9328 <MDL 7.5420 25.6933 8.8655 2.4580 8.6555 312.185

Mb3 2.2622 <MDL 3.9443 24.1763 6.3689 1.7285 4.7448 408.353

Mb4 2.0376 0.1803 5.0235 27.9467 7.7978 2.3354 6.0502 388.166

Mb5 2.5620 <MDL 4.7727 26.2087 6.4153 1.8079 5.0723 325.103

Mb6 2.1458 0.1983 5.3120 25.3294 7.2245 2.2041 5.5627 329.096

Mb7 2.0776 0.0416 6.0803 25.1247 8.8227 2.8255 7.8532 339.335

Mb8 2.0394 0.1538 3.1234 22.4258 5.1735 1.4741 3.1843 244.794

Mb9 1.6175 0.1720 4.0008 19.0704 5.5733 1.6912 4.5045 317.936

Mb10 3.2754 0.1373 3.5258 26.3691 5.2262 1.4984 4.0509 268.740

Mb11 1.8399 <MDL 1.5588 18.7564 3.5434 1.0562 1.7376 173.850

Sample #

 Content (ug) ==> Mb1 0.0130 <MDL 0.0410 0.1327 0.0505 0.0135 0.0497 1.6130

Mb2 0.0184 <MDL 0.0718 0.2446 0.0844 0.0234 0.0824 2.9720

Mb3 0.0217 <MDL 0.0378 0.2316 0.0610 0.0166 0.0454 3.9111

Mb4 0.0236 0.0021 0.0583 0.3242 0.0905 0.0271 0.0702 4.5027

Mb5 0.0413 <MDL 0.0770 0.4228 0.1035 0.0292 0.0818 5.2450

Mb6 0.0368 0.0034 0.0911 0.4344 0.1239 0.0378 0.0954 5.6440

Mb7 0.0500 0.0010 0.1463 0.6047 0.2123 0.0680 0.1890 8.1667

Mb8 0.0950 0.0072 0.1455 1.0447 0.2410 0.0687 0.1483 11.4033

Mb9 0.0988 0.0105 0.2443 1.1643 0.3403 0.1033 0.2750 19.4100

Mb10 0.2028 0.0085 0.2183 1.6323 0.3235 0.0928 0.2508 16.6350

Mb11 0.1080 <MDL 0.0915 1.1010 0.2080 0.0620 0.1020 10.2050

105
106

Appendix D

Concentrations of Hg and Se in surface sediments and the clam Macoma petalum from Palo Alto (D1a, D-1b) and in standard reference materials (D-2). 
107

D-1a. Mercury and selenium concentrations (μg/g dry weight) determined in surface sediments and 

M. petalum in 2005. One analysis was conducted on homogenized sediment. Values for M. petalum

are the mean and 95% confidence interval (n=3). Not analyzed (NA). 

Date Sediment M. petalum 

mercury selenium mercury selenium

January 18, 2005 0.32 0.5 0.39±8E-17 5.9±0.77

February 15, 2005 0.31 0.4 NA NA 

April 25, 2005 0.32 0.4 0.15±0.05 4.7±0.79

June 28, 2005 0.28 0.3 0.12±0.05 4.2±0.43

September 20, 2005 0.26 0.3 0.29±0.14 5.5±1.3 

D-1b. Mercury and selenium concentrations (μg/g dry weight) determined in sample splits of surface 

sediments and M. petalum collected in April 2005. 

Date Sediment M. petalum 

mercury selenium Mercury selenium

April 25, 2005 0.32/0.33 0.4/0.5 0.17/0.19 5.4/5.6 
108

D-2. Observed and certified concentrations of mercury and selenium in standard reference materials 

analyzed in 2005. Certified concentrations as reported by National Research Council Canada are the 

mean and 95% confidence interval. The three materials are marine sediments (MESS-3), dogfish 

liver (DOLT-2), and dogfish muscle (DORM-2). 

SRM Mercury Selenium 

Observed Certified Observed Certified 

MESS-3 0.08 0.09±0.01 0.8 0.7±0.1 

DOLT-2 2.1 2.14±0.28 6.6 6.1±0.5 

DORM-2 4.5 4.64±0.26 1.5 1.4±0.1 
109

Appendix E 

Results of the analyses of National Institute of Science and Technology (NIST) standard reference 

materials for elements, excluding selenium and mercury. Recoveries are reported as the observed 

concentrations and the percent recoveries relative to the certified values for the standard. Results for 

SRM 2709 (San Joaquin Soil) are shown in E-1, for SRM 2976 (mussel tissue) in E-2, and E-3, 

respectively. 
110

E-1. Observed and certified concentrations in SRM 2709. Units in upper table are μg/mL. The lower table reports the percent 

recovery.

Month Rep AL CR CU FE MN NI PB V ZN

January 1 57566.897 126.62 35.80 40093.92 1075.67 82.04 31.88 136.90 137.52

2 58160.804 131.36 34.19 41356.78 1095.48 84.45 32.44 132.36 139.40

February 1 55318 121.90 33.05 39563.98 1150.71 79.29 31.35 128.82 130.71

2 56530 125.47 33.63 40076.94 1172.82 80.77 31.19 127.44 133.66

March 1 58882.098 135.25 35.33 41630.52 1127.76 84.91 33.20 134.17 139.69

2 56675.263 127.36 35.41 41628.65 1136.68 85.73 33.35 131.22 140.55

April 1 54862.768 122.81 34.71 39309.86 1247.02 79.04 30.45 129.47 131.46

2 55747.863 124.79 34.34 39839.74 1255.34 79.74 30.72 131.52 131.20

May 1 44916.245 116.28 28.40 34086.48 511.98 65.29 23.66 106.16 107.13

2 44562.842 114.94 28.28 33606.56 507.10 64.40 23.84 105.28 106.19

June 1 43493.395 118.44 26.08 31970.72 665.92 61.61 23.09 97.55 101.93

2 43474.918 115.99 25.63 32317.89 673.55 61.71 23.82 102.34 100.04

September 1 34007 89.74 21.15 30391.96 541.84 59.86 22.74 64.57 92.78

2 30082 79.01 21.23 28281.72 511.70 56.20 21.32 52.55 87.93

October 1 32735 88.72 22.64 30529.41 595.49 60.89 23.78 52.74 94.24

Decem

2 32713 88.56 22.41 29649.31 574.21 58.92 22.89 59.72 93.43

ber 1 42318.18 102.09 29.52 35418.18 821.27 73.74 27.64 71.18 119.82

2 44008.75 106.88 30.79 35746.85 823.09 74.30 27.87 74.07 122.01

Cert. Value 75000 130.00 34.60 35000 538 88.0 18.9 112.0 106.0

Std 0 4.00 0.70 0 17 5.0 0.5 5.0 3.0

Month Rep AL CR CU FE MN NI PB V ZN

ary 1 77 97.40 103.46 115 200 93.23 168.68 122.23 129.73

2 78 101.04 98.82 118 204 95.97 171.65 118.18 131.51

ry 1 74 93.77 95.53 113 214 90.10 165.85 115.01 123.31

2 75 96.51 97.18 115 218 91.78 165.02 113.79 126.09

ch 1 79 104.04 102.11 119 210 96.49 175.67 119.79 131.78

2 76 97.97 102.34 119 211 97.42 176.44 117.16 132.59

l 1 73 94.47 100.31 112 232 89.82 161.11 115.60 124.02

2 74 95.99 99.24 114 233 90.62 162.52 117.43 123.77

1 60 89.45 82.08 97 95 74.19 125.16 94.78 101.07

2 59 88.41 81.73 96 94 73.18 126.16 94.00 100.18

e 1 58 91.11 75.38 91 124 70.01 122.17 87.10 96.16

2 58 89.22 74.07 92 125 70.13 126.05 91.38 94.38

ptember 1 45 69.03 61.13 87 101 68.02 120.29 57.65 87.53

2 40 60.77 61.36 81 95 63.87 112.82 46.92 82.96

tober 1 44 68.24 65.43 87 111 69.20 125.84 47.09 88.90

2 44 68.12 64.76 85 107 66.95 121.12 53.32 88.14

ber 1 56 78.53 85.31 101 153 83.79 390.14 24.68 67.15

2 59 82.21 88.98 102 153 84.43 147.45 66.13 115.11

AVG 63 87.02 85.51 102 160 81.62 159.12 89.01 108.02

STDEV 13 12.91 15.31 13 54 11.91 61.99 31.64 20.61

Janu

Februa

Mar

Apri

May

Jun

Se

Oc

Decem
E-2. Observed and certified values for inorganic elements in NIST Standard Reference Material 2976 (mussel tissue) 

Values for different dates are the observed mean concentrations and 1 standard deviation for either replicate or triplica(n=2-3). The mean values are summarized as the median. The certified values for the standard reference material are 

observed values (vanadium is not certified for this material). All values are reported as μg/g dry weight. Standards for be analyzed because of a processing error. 

Date prepared Cadmium Chromium Copper Lead Nickel Silver Vanadi01/18/2005 0.65±0.01 0.51±0.01 4.18±0.02 0.58±0.02 0.97±0.01 <MDL 0.64±002/15/2005 0.66±0.01 0.61±0.05 4.29±0.09 0.59±0.01 0.98±0.02 0.015 0.67±003/07/2005 0.66±0.02 0.58±0.02 4.40±0.1 0.59±0.06 1.00±0.02 <MDL 0.68±0 04/25/2005 0.61±0.01 0.62±0.08 4.40±0.02 0.58±0.08 0.97±0.02 <MDL 0.69±005/25/2005 0.62±0.01 0.54±0.15 4.39±0.17 0.56±0.04 1.00±0.01 <MDL 0.69±006/28/2005 0.60±0.01 0.53±0.08 4.31±0.1 0.57±0.01 0.95±0.03 <MDL 0.70±011/01/2005 0.63±0.01 0.43±0.01 4.02±0.01 0.62±0.01 0.85±0.01 <MDL 0.69±012/13/2005 0.68±0.05 0.34±0.03 4.20±0.35 0.61±0.08 1.01±0.08 <MDL 0.65±0Median 0.64 0.54 4.30 0.59 0.98 0.015 0.69 Certified Value Mean 0.82 0.50 4.02 0.93 1.19 0.011 Not cer95% CI 0.16 0.02 0.33 0.12 0.18 0.005 

111
E-3. Percent recovery of inorganic elements in NIST Standard Reference Material 2976 (mussel tissue) prepared in 20

reported as the percent of the certified mean concentration, and are the means of duplicate or triplicates (n=2-3) of the Date prepared Cadmium Chromium Copper Lead Nickel Silver Vanadi01/18/2005 79 102 104 81 63 NA NA 02/15/2005 80 121 107 82 63 140 NA 03/07/2005 80 115 109 84 63 NA NA 04/25/2005 75 123 109 82 62 NA NA 05/25/2005 75 107 109 84 60 NA NA 06/28/2005 74 105 107 79 61 NA NA 11/01/2005 76 86 100 72 66 NA NA 12/13/2005 82 70 104 85 66 NA NA Mean 78 104 106 81 63 Median 78 106 107 82 63 

112
Appendix F

Method detection limits (MDL) and reporting levels (MRL) for the analysis of sediment and tissue samples by ICP-OE

in units of μg/mL. 

113
F-1. Method detection limits and reporting levels for ICP-OES methods. Concentration markers are method detection 

method reporting level (MRL). All units are μg/mL. Elements for which MDL and MDL were not determined in a padesignated ND. Method marker Ag Al Cd Cr Cu Fe Mn Ni Pb Sediment: near-total digestion MDL ND 0.007 ND 0.001 0.003 0.008 0.001 0.001 0.003 

MRL ND 0.020 ND 0.004 0.01 0.020 0.002 0.003 0.009 

Sediment: partial extraction MDL 0.001 0.020 ND 0.002 0.003 0.005 0.001 0.0004 0.001 

MRL 0.002 0.060 ND 0.007 0.01 0.020 0.002 0.001 0.004 

Tissue MDL 0.001 ND 0.0002 0.004 0.001 ND ND 0.001 0.002 

MRL 0.002 ND 0.0003 0.007 0.002 ND ND 0.002 0.004 

114
Appendix G 

Reproduction data for the year 2005 (G-1). 

115
G-1. Reproductive stage of M. petalum sampled from Palo Alto during 2005. 

Date of sample Inactive Active Ripe Spawning Spent n Reproductive Nonreproductive January 18 0.0 0.0 100.0 0.0 0.0 10 100 0 February 15 0.0 0.0 100.0 0.0 0.0 10 100 0 March 7 0.0 0.0 20.0 80.0 0.0 10 100 0 April 25 0.0 0.0 10.0 60.0 30.0 10 70.0 -30 May 25 0.0 0.0 45.5 27.3 27.3 11 72.7 -27 June 28 0.0 41.7 25.0 0.0 33.3 12 66.7 -33 September 20 0.0 0.0 0.0 30.0 70.0 10 30.0 -70 November 1 0.0 81.8 18.2 0.0 0.0 11 100 0 December 13 0.0 0.0 100.0 0.0 0.0 10 100 0 

116
Appendix H 

Complete list of benthic species found at Palo Alto in the year 2005. 

117
Species

Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean St

Acari 000000000000000Ampelisca abdita 3.3 0.6 2.7 1.5 2.3 2.1 0.3 0.6 1.0 0.0 2.3 1.5 0.7 1.2 2.3 Ampithoe spp. 000000000000000Anthozoa 000000000000000Balanus ?aquila 000000000000000Balanus improvisus 000000000000000Balanus spp. 000000000000000Boonea bisuturalis 0 0 0.3 0.6 0.3 0.6 0.7 0.6 0.3 0.6 0.3 0.6 2.0 2.0 0.3 Calinoida 0 0 0 0 0.3 0.6 0.7 1.2 0 0 0 0 0 0 0 Callianassidae 000000000000000Capitella "capitata" 0 0 0 0 0 0 0 0 0.3 0.6 0 0 0 0 0 Caprella californica 000000000000000Cirratulidae 000000000000000Cirripedia 000000000000000Corophium ?insidiosum 0.7 1.2 0 0 0 0 0 0 0 0 0 0 0 0 0 Corophium acherusicum 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Corophium insidiosum 000000000000000Corophium spinicorne 000000000000000Corophium spp. 0 0 0.3 0.6 0.3 0.6 0 0 0 0 0 0 0 0 0 Corophium spp. (female & juvenile) 2.3 1.5 0 0 0.3 0.6 0 0 0 0 0.7 1.2 0.3 0.6 0 Corophium spp. (male) 000000000000000Cumella vulgaris 000000000000000Cyprideis spp. 0 0 0 0 0 0 0.3 0.6 0.3 0.6 0 0 0 0 0 Dynamenella spp. 000000000000000Eogammarus confervicolus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Eteone ?californica 0 0 0 0 0 0 0.3 0.6 5.3 9.2 0 0 0 0 0 Eteone lighti 3.3 1.5 1.7 1.5 1.3 1.5 4.7 3.1 4.7 5.7 4.7 3.1 1.3 1.5 4.0 Eteone spp. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 

1/5/2005 2/15/2005 3/7/2005 4/25/2005 5/25/2005 6/27/2005 7/20/2005 8/18/20

118
Species

Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean St

Euchone limnicola 0 0 0 0 0 0 000000000Euchone spp. 0 0 0 0 0 0 000000000

Eusarsiella zostericola 5.0 2.6 2.3 1.5 4.0 3.5 7.7 2.5 3.0 1.7 0.3 0.6 0 0 1.3 Gemma gemma 37.7 2.9 36.7 2.1 41.3 13.6 56.3 4.5 18.7 21.4 133.0 20.0 213.7 58.8 638.7 1Glycera spp. 000000000000000Glycinde armigera 000000000000000Glycinde polygnatha 000000000000000Glycinde spp. 0 0 0 0 0 0 2.7 0.6 0 0 0 0 0 0 0 Gnorisphaeroma oregonensis 0 0 0 0 0 0 000000000Grandidierella japonica 3.7 2.1 0 0 0.7 0.6 0.3 0.6 0 0 16 13.5 6.0 2.6 1.0 Harmothoe imbricata 0 0 0 0 0 0 000000000

Harpacticoida 000000000000000Hemigrapsus oregonensis 0 0 0 0 0 0 000000000Heteromastus filiformis 21.0 6.1 21.0 7.5 12.3 10.7 14.7 5.1 16.3 10.0 20.3 2.5 19.7 3.2 16.7 Ilyanassa obsoleta 000000000000000Macoma petalum 5.3 4.0 5.0 3.0 3.7 2.1 6.0 1.0 5.7 4.0 4.7 2.5 5.7 4.0 7.3 Macoma spp. 000000000000000Marphysa sanguinea 000000000000000Melita nitida 000000000000000Musculista senhousia 0 0 0 0 0 0 000000000

Mya arenaria 0 0 0 0 0 0 1.0 1.0 0.7 0.6 0 0 0 0 0 Mysidacea 000000000000000Naididae 000000000000000Neanthes succinea 1.0 1.7 3.0 1.0 3.7 1.2 1.0 0 0 0 0 0 1 0 1.3 Nematoda 0 0 0 0 1.3 1.5 1.3 0.6 2.0 2.6 0 0 3.7 4.0 3.0 Nippoleucon hinumensis 38.3 11.0 17.0 9.8 19.0 0 117.0 32.0 212.3 70.4 46.3 9.7 110.3 8.7 69.7 3Odostomia fetella 2.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Odostomia spp. 0 0 0.3 0.6 2.7 1.2 3.7 1.5 3.3 1.2 1.3 1.5 1.3 1.5 1.0 Oligochaeta 0 0 0 0 0 0 000000000

1/5/2005 2/15/2005 3/7/2005 4/25/2005 5/25/2005 6/27/2005 7/20/2005 8/18/20

119
Species

Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean Stdev Mean St

Planariidae A 0.3 0.6 3.3 4.2 0 0 0.3 0.6 0 0 0 0 0 0 0 Polydora cornuta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.3 Polydora spp. 000000000000000Potamocorbula amurensis 0 0 0 0 0 0 1.7 0.6 6.0 6.0 4.3 2.5 4.7 1.5 2.3 Pseudopolydora kempi 000000000000000Rochefortia grippi 000000000000000Rochefortia spp. 000000000000000Sabaco elongatus 000000000000000Sphaeromatidae (juv.) 000000000000000Sphaerosyllis californiensis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Sphaerosyllis erinaceus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Streblospio benedicti 9.0 2.6 14.7 8.0 13.3 4.5 20.0 9.5 24.0 5.0 3.7 2.5 8.7 3.5 11.3 Synidotea laevidorsalis 000000000000000Tellinidae 000000000000000Tharyx spp. ? 0 0 0.7 0.6 1.0 1.7 0 0 0.3 0.6 0.7 0.6 1.0 1.0 0 Tubificidae 13.3 5.5 12.3 11.1 22.7 23.8 27.3 15.2 15.3 11.4 11.0 10.1 31.0 19.0 22.3 3Turbellaria 000000000000000Unid. Actiniaria 0 0 0 0 0.7 1.2 0 0 0 0 0 0 0.3 0.6 0.3 Unid. Amphipod 000000000000000Unid. Balanomorpha 000000000000000Unid. Bivalvia 000000000000000Unid. Cumacea 000000000000000Unid. Gastropoda 000000000000000Unid. Isopoda 000000000000000Unid. Nudibranchia 000000000000000Unid. Ostracoda 000000000000000Unid. Polychaeta 000000000000000Unid. Spionidae 000000000000000Unid. Syllidae 000000000000000Unid. Tanaidacea 000000000000000Urosalpinx cinerea 000000000000000

1/5/2005 2/15/2005 3/7/2005 4/25/2005 5/25/2005 6/27/2005 7/20/2005 8/18/20

120