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: 2006 

U.S. GEOLOGICAL SURVEY 

OPEN FILE REPORT 2007-1199 

Prepared in cooperation with the 

CITY OF PALO ALTO, CALIFORNIA 

U.S. Department of the Interior 

U.S. Geological Survey 
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: 2006 

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

Luoma, Michelle I. Hornberger, Jessica L. Dyke, Raul Cervantes, and Michelle K. 

Shouse 

U.S. GEOLOGICAL SURVEY 

OPEN FILE REPORT 2007-1199 

Prepared in cooperation with the 

CITY OF PALO ALTO, CALIFORNIA 
ii

U.S. DEPARTMENT OF THE INTERIOR 

DIRK KEMPTHORNE, Acting Secretary 

U.S. GEOLOGICAL SURVEY 

Mark Myers, 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.usgs.gov/of/2007/1199

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 
iii

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 ............................................................................................................................ 13

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

Summary ............................................................................................................................................................................ 16

Long-term Observations .............................................................................................................................................. 16

2004-2006 ........................................................................................................................................................................ 17

Value of Long-Term Monitoring ................................................................................................................................. 17

References ........................................................................................................................................................................ 18

Figures ................................................................................................................................................................................ 23

Tables ................................................................................................................................................................................. 73

Appendix A ........................................................................................................................................................................ 79

Appendix B ........................................................................................................................................................................ 83

Appendix C ......................................................................................................................................................................... 89

Appendix D ...................................................................................................................................................................... 108

Appendix E ....................................................................................................................................................................... 111

Appendix F ....................................................................................................................................................................... 114

Appendix G ...................................................................................................................................................................... 116

Appendix H ...................................................................................................................................................................... 118

 
iv

List of figures 

Figure 1. Location of the Palo Alto sampling site in South San Francisco Bay. ................................................... 24

Figure 2. Precipitation ...................................................................................................................................................... 25

Figure 3. Water column salinity ..................................................................................................................................... 26

Figure 4. Aluminum, iron and silt/clay in sediments ................................................................................................... 27

Figure 5. Chromium, nickel and vanadium in sediments ........................................................................................... 28

Figure 6. Copper in sediments ........................................................................................................................................ 29

Figure 7. Correlation between copper effluent from PARWQP and copper concentrations in 

surface sediments ............................................................................................................................................................ 30

Figure 8. Zinc in sediments ............................................................................................................................................. 31

Figure 9. Silver in sediments........................................................................................................................................... 32

Figure 10. Selenium and mercury in sediments .......................................................................................................... 33

Figure 11. Annual mean copper in Macoma petalum ................................................................................................ 34

Figure 12. Annual mean silver in Macoma petalum ................................................................................................... 35

Figure 13. Correlation between copper loadings from the PARWQP and copper concentrations in 

Macoma petalum ............................................................................................................................................................. 36

Figure 14. Copper in Macoma petalum ......................................................................................................................... 37

Figure 15. Silver in Macoma petalum ........................................................................................................................... 38

Figure 16. Chromium in Macoma petalum ................................................................................................................... 39

Figure 17. Nickel in Macoma petalum .......................................................................................................................... 40

Figure 18. Zinc in Macoma petalum .............................................................................................................................. 41

Figure 19. Mercury in Macoma petalum ...................................................................................................................... 42

Figure 20. Selenium in Macoma petalum ..................................................................................................................... 43

Figure 21. Condition index of Macoma petalum ......................................................................................................... 44

Figure 22. Reproductive activity of Macoma petalum ............................................................................................... 45

Figure 23. Reproductive activity of Macoma petalum 2000 thru 2006. .................................................................... 46

Figure 24. Total number of species present ................................................................................................................ 47

Figure 25. Total average number of individuals present ........................................................................................... 48

Figure 26. Average abundance of Macoma petalum ................................................................................................. 49

Figure 27. Average abundance of Mya arenaria ........................................................................................................ 50

Figure 28. Average abundance of Gemma gemma .................................................................................................... 51

Figure 29. Average abundance of Ampelisca abdita ................................................................................................. 52

Figure 30. Average abundance of Streblospio benedicti .......................................................................................... 53

Figure 31. Average abundance of Grandiderella japonica ....................................................................................... 54

Figure 32. Average abundance of Neanthes succinea ............................................................................................. 55

Figure 33. Average abundance of Heteromastus filiformis ...................................................................................... 56

Figure 34. Average abundance of Nippoleucon hinumensis ................................................................................... 57

Figure 35. Heteromastus filiformis abundance with silver and copper in Macoma petalum. ............................ 58

Figure 36. Heteromastus filiformis annual abundance with silver in M. petalum and sediment ....................... 59

Figure 37. Heteromastus filiformis annual abundance with copper in M. petalum and sediment .................... 60

Figure 38. Ampelisca abdita abundance with silver and copper in M. petalum ................................................... 61

Figure 39. Ampelisca abdita annual abundance with silver in M. petalum and sediment ................................. 62

Figure 40. Ampelisca abdita annual abundance with copper in M. petalum and sediment .............................. 63
v

Figure 41. Streblospio benedicti abundance with silver and copper in M. petalum ............................................ 64

Figure 42. Streblospio benedicti annual abundance with silver in M. petalum and sediment. ......................... 65

Figure 43. Streblospio benedicti annual abundance with copper in M. petalum and sediment ....................... 66

Figure 44. Gemma gemma abundance with silver and copper in M. petalum ...................................................... 67

Figure 45. Gemma gemma annual abundance with silver in M. petalum and sediment. .................................... 68

Figure 46. Gemma gemma annual abundance with copper in M. petalum and sediment .................................. 69

Figure 47. Benthic community rank-abundance data for 2006 ............................................................................... 70

Figure 48. Benthic community rank-abundance data for 1977, 1989, 2002, and 2006. Feeding mode 

for each species at each rank is shown. ..................................................................................................................... 71

Figure 49. Benthic community rank-abundance data for 1977, 1989, 2002, and 2006. ........................................ 72

List of tables 

Table 1. Sediment characteristics and salinity in 2006 ............................................................................................ 74

Table 2. Concentrations of trace elements in sediments in 2006 ............................................................................ 75

Table 3. Annual mean copper in Macoma petalum and sediments 1977 through 2006 ..................................... 75

Table 4. Annual mean silver in Macoma petalum and sediments 1977 through 2006 ........................................ 77

Table 5. Concentrations of trace elements in Macoma petalum in 2006. .............................................................. 78

Conversion Factors, Abbreviations, and Acronyms 

Conversion Factors 

Multiply By To obtain

foot (ft)  

l) 

0.3048 meter

gallon (ga 3.785 liter (L)

inch (in.)   2.54  centimeter

inch (in.)  

M) 

25,400 

weight

micrometer (μm)

micromolar (μ rams per liter

)  

molecular 

000 

microg

micron (μm 1,000, meter

mile (mi)   1.609  r

.35 

kilomete

ounce (oz) 

part per million 

28

1 

gram (g)

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 
vi

Abbreviations and Acronyms 

Abbreviations and Acronyms Meaning

CI  Condition Index

ERL  Effects Range‐Low 

ERM 

ES 

Effects Range‐Median

ICP‐O 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 

P 

National Pollutant Discharge Elimination System  

PARWQC

CB 

Palo Alto Regional Water Quality Control Plant 

RWQ 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: 2006 

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

Michelle I. Hornberger, Jessica Dyke, Raul Cervantes, and Michelle Shouse 

Abstract 

Results reported herein include trace element concentrations in sediment and in the clam 

Macoma petalum (formerly reported as Macoma balthica (Cohen and Carlton 1995)), clam 

reproductive activity, and benthic macroinvertebrate community structure 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 2006 to December 

2006, 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 2006 were consistent with 

results observed since 1990. Most notably, copper and silver concentrations in sediment and 

clam tissue increased in the last year but the values remain well within range of past data. Other 

metals such as chromium, nickel, vanadium, and zinc remained relatively constant throughout 

the year except for maximum values generally occurring in winter months (January-March). 

Mercury levels in sediment and clam tissue were some of the lowest seen on record. Conversely, 

selenium concentrations reached a maximum level but soon returned to baseline levels. In all, 

metal concentrations in sediments and tissue remain within past findings. There are no obvious 

directional trends (increasing or decreasing). 

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 biosentinel clam M. 

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 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 
2

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 nonindigenous filter-feeding clam 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). 

Biological Response to Trace Metals 

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

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

in changes at the population level, such as reductions in growth, survival and reproductive 
3

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 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 (Alpine and Cloern 1992 provides a local example). 

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

stages through a variety of routes - sediment, water and food (Wang and Fisher 1999 provides a 

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

to contaminant concentration as well as duration. Even at 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 levels. 

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 M. 

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 include 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; 2005; Shouse and others 2003; 2004; Thompson and others 2002; Cain and others 

2006) were used to meet the following objectives: 

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

sediments and clams, reproductive activity of clams and benthic-community structure at a 

site designated in the RWQCB's Self-Monitoring Program guidelines for PARWQCP 

• Present the data within the context of historical changes in South 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 
4

• 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, M. petalum. 

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

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

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

others 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 M. petalum

provides a direct measure of exposure to bioavailable metals. 

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

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

concentrations of metals in the tissues of M. petalum were compared with physiological 

indicators. Two common animal responses to environmental stress are reduced 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). In addition, the benthic community 

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

macroinvertebrate community resulting in a change in the function of the community. We 

hypothesized that a shift in community composition and potentially in function of the benthic 

community in the ecosystem would result from changes in the concentrations of specific metals 

or from a composite of all contaminants for several reasons. First, prior studies have shown that 

South Bay benthic communities were dominated by opportunistic species in the 1980s (see 

Nichols and Thompson 1985a). This opportunistic species might become less dominant as 

environmental stressors decrease. Second, environmental pollutants may differentially affect 

benthic species that use different feeding and reproductive modes. An intertidal mudflat 

community, such as this study site, should include a combination of species that feed on particles 
5

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

Any absence of one of these feeding groups may show limitations on species due to 

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

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

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

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

community and measured environmental parameters (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 adjacent to Sand Point on a mudflat on the western shore 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; 2005; Shouse and others 2003; 

2004; Thompson and others 2002; Cain and others 2006). 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 2006, 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 

data (1974 through 1983; Nichols and Thompson 1985a, 1985b) showed that when differences 
6

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 2006. 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 mesh polyethylene screen 

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

mesh size was chosen to match the largest grains typically found in the digestive tract of M. 

petalum. All 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 

Cain and others 2005; 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 g. 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 

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 
7

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 

M. 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 g wet weight. To meet this 

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

form broader size classes (within 3-4 mm of each other as appropriate). Once the composites 

were formed, the clams were dissected as described above, and the soft tissue was placed into 

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 (approximately 18 M 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). 
9

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 2006. 

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 (Weesner, 

1960). Sections were stained with Harris’ hematoxylin and eosin and examined with a light 

microscope. Each individual was characterized by size (length in mm), sex, developmental stage, 

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

classes of gonadal development (previously described by Parchaso, 1993) (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 taken arbitrarily, 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) 
10

(Figure 2). The 12 year (1994-2006) average annual rainfall is 24.6 inches. At 29.5 inches, 

precipitation for 2006 was slightly above average. Within the three year period 2004-2006 

rainfall ranged from 23.2 (2004) to 33.1 (2005). Rainfall during March and April of 2005 and 

2006 was especially elevated compared to the average. 

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 2006. The salinity 

minimum of 8 parts per thousand (ppt) occurred in April, consistent with the late season rainfall 

and elevated inflow of freshwater from surface water runoff. This was the lowest spring time 

salinity since 2000. Salinities continually increased during the dry season and reached their 

maximum (25 ppt) in the fall (October). 

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 summer and fall. The authors 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 2006 (Figure 4, Appendix A). 

In 2006, the percent of silt/clay in the sediment was at its maximum (87%) in April and 

declined to 35% in May following prolonged spring rainfall. Aluminum and Fe concentrations 

generally 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 (values from January through April averaged 1.4%) compared with the balance of the 

year (average 1.1%). 

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 (52 μg/g in October) and the 

following winter/spring maximum in 2005 (85 μg/g in March) were the lowest seasonal 

concentrations observed. This pattern was broken in 2006, as minimum levels in June (68 μg/g) 

were more typical of the record. 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 

(42% - 93% of the time for different metals). It must be remembered, however, that these effects 
11

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

toxicity. In 2005, Cu concentrations were near or below the ERL (34 μg/g) for the entire year, 

the first time this has been observed. However, in 2006, the concentrations increased to the 

highest levels observed since 2000 and exceeded the ERL for the entire year. The typical 

seasonal pattern was observed in 2006. Cu concentrations peaked in January (55 μg/g) and then 

gradually declined throughout the year. The minimum concentration (37 μg/g) was observed 

earlier in the year (June) compared to past years which typically occurred in fall/winter months 

(Figure 6, Table 2) Near-total Cu concentrations appear to have been declining gradually since at 

least 2000. Over the same period, partial-extractable concentrations have remained relatively 

constant outside of the typical seasonal variation (Figure 6). 

Copper concentrations in the surface sediments (for all years (1977-2006)) were highly 

correlated with copper loadings in effluent from the PARWQP, driven by the 1977-1988 data 

(r2

= 0.77, p<0.0001 Figure 7). However, since 1989, the variability observed in the sediments 

has not correlated well with the generally low copper loadings (r2= 0.29 Figure 7) and is 

indicative of the influence by other factors. 

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

below the Zn ERL (150 μg/g) (Figure 8, Table 2) with the exception of January 2006. 

Concentrations in that sample were the highest ever observed (310 μg/g), but were consistent in 

high concentrations of other elements. The concentration immediately returned below the ERL in 

February. 

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 (regional background) (Hornberger and others, 1999) (Figure 9, Table 2). 

The seasonal pattern observed in 2005 was not evident in Ag concentrations in 2006. In that 

year, Ag concentrations were exceptionally stable. Long term directional trends in the annual 

mean concentrations were not evident. 

Mercury concentrations in sediment during 2006 ranged between 0.2 μg/g (January) to 

0.3 μg/g (December) (Figure10, Table 2). These are amongst the lowest ever observed in the 

record (1994-2006). Conversely, in April of 2004, concentrations of Hg in the sediment (0.5 

μg/g) were 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 have increased slightly in the past four years (annual means 0.4 

μg/g, 0.4 μg/g, 0.4 μg/g, and 0.5 μg/g respectively) but remain within the overall range of data 

since analysis of this element in 1994 (Figure 10, Table 2). Increasing concentrations of 

selenium vary in magnitude from year to year. In 2006, concentrations ranged between 0.4 μg/g 

(May and December) to 0.8 μg/g (January). 

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 (Figure 11 and Figure 12, 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. Concentrations were particularly low and 

stable from 1997 through 2005. Annual mean concentrations of Cu and Ag for 2006 were, 

respectively, 45 ± 8 and 3.8 ± 0.8 μg/g, a two-fold increase from 2005, but still within the error 

of means from recent years (2002-2004 for copper and 1997-2002 for silver). Copper 

concentrations in the clams were highly correlated with copper loadings in PARWQP effluent 
12

for all years,1977-2006, driven by the high concentrations and loadings in 1977-1988 (r2= 0.90, 

p<0.0001 Figure13). However, in recent years (1989-2006), inter-annual variation in copper 

concentrations in the clam do not correlate with copper loadings (r2= 0.10 Figure 13). 

Intra-annual variations in Ag and Cu 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 (Figure14, Figure15). 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 December, concentrations were only about half the maximum values observed in 2004. 

Then in 2006, concentrations increased steadily throughout the year, reaching a maximum 

concentration in November (83 μg/g for Cu and 7.9 μg/g for Ag). Concentrations this high have 

not been observed since 1997. 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 16, Table 5), Ni (Figure17, Table 

5) and Zn (Figure18, 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 - 2006). 

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 2006. In addition to the 

typical seasonal pattern, Zn concentrations exhibited a slight long-term decline through 2005. 

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

to subsequent years. However, in 2006, concentrations increased notably to values comparable to 

those observed in the mid to late 90s. Wellise and others (1999) observed that seasonal and interannual 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. 

Before 2006, mercury concentrations in M. petalum, like Zn, have trended slightly lower 

since 1994 (Figure19). The highest concentrations observed during the record occurred in 

September 1994 and during the winters of 1995 and 1996 (all 0.5 μg/g). The seasonal 

(summer/fall) low concentration in 1995 (0.3 – 0.4 μg/g) was the highest recorded, also. 

Concentrations declined after 1996 and reached the minimum value in 2005. Concentrations in 

2006 returned to the maximum concentrations observed in 1994 and 1995. 

Selenium concentrations in M. petalum vary seasonally like other elements (Figure20, 

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 

2006 appear consistent with this more recent feature. 

The condition index for M. petalum at Palo Alto extends back to 1988 (Figure21). 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. Since 2003 the maximum CI has 

steadily declined. In 2006, the maximum CI was one of the lowest observed. 
13

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 (and perhaps Cu) 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 of M. petalum improved (Figure22). Furthermore, the low 

reproductive activity observed during the late 1970s has not been observed during the entire 

period of reduced metal exposures. Data for 2006 show that M. petalum continues to be highly 

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

active at any time during the normal seasonal cycle of reproduction which begins in fall with 

spawning occurring the following spring (see Appendix G for detailed reproduction data for 

2006 and Figure 23 for short term history of reproduction). 

Benthic Community 

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

in assessing environmental stress on biological communities. Species diversity, as estimated by a 

time series of number of species, has remained consistent throughout the recent study with the 

exception of small temporary increases as seen in 2006 (Figure 24). Total animal abundance 

shows the same trend (Figure 25). 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. In general, the species composition has changed little in 2006 relative 

to that seen in 2004 and 2005. 

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

shown any consistent trend over the 30-year period and did not show any significant deflection 

from the norm in 2006 (Figure26, Figure27, and Figure28). There was significant seasonal and 

inter-annual variability in species abundances for all species and that is well illustrated in these 

three bivalves. There were six species that did show trends in their abundance throughout the 

study and these trends continued through the 2004-2006 period. The first species, Ampelisca 

abdita, is a small crustacean that lives above the surface of the mudflat in a tube built from 

selected sediment particles. A. abdita showed a general decline in both the annual average 

abundances and annual maximum abundances (seasonal peaks in abundance; Figure29). The 

second species to show 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 annual 

maximum abundances declined, as well as annual average abundances (Figure 30). The 

maximum seasonal abundance of the small burrowing crustacean Grandiderella japonica, a 

deposit feeder, declined through the 1980s but has since become more abundant (Figure 31). 

Neanthes succinea, a burrowing polychaete that feeds on surface deposits and scavenges for 

detrital food, similarly showed large seasonal fluctuations in abundance through the 1980s. N. 

succinea abundance had increased by the late 1990s and the annual average abundances and 

annual maximum abundances (Figure 32) remained relatively stable until 2005 and 2006 when 

the abundance decreased. Two species showed an increase in abundance within the time series. 

The first was the polychaete worm Heteromastus filiformis (Figure 33), a deposit feeding, 

burrowing species that lives deep in the sediment (usually 5-20 cm below the surface of the 
14

mudflat). Abundance increased sharply in 1985 and then partially receded in the late 1980s. 

Abundances since 2000 have remained higher than in the late 1970s and 2006 abundance was 

similar to those seen since 2002. The second species showing an increase was Nippoleucon 

hinumensis, a small burrowing crustacean, which appeared in the dataset in 1988 (Figure 34)

following its introduction into the bay in 1986 (Cohen and Carlton 1995). Corbula amurensis, a 

non-indigenous filter feeding bivalve, first appeared in the benthic community in significant 

numbers in April 2005 and persisted into 2006 with peaks in abundance occurring in spring and 

fall (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. Comparison of 

metal concentration and benthic species abundance 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 35). 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 

36) and (Figure 37). To interpret these plots, we must first 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 others 1995). 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 nine years of data since the 

early 1990s, 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 (Figure38, Figure39 and Figure40) and the worm S. benedicti (Figure 

41, Figure42, and Figure 43) 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 
15

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

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

abundance of G. gemma (Figure 44, Figure45, and Figure 46), the small clam that reproduces 

by brooding their young and lives on the sediment surface. However, G. gemma returned to 

much lower numbers in 2006 following a very large abundance peak in 2005. All three species 

are suspension feeders and thus consume water borne particles, although S. benedicti may also 

deposit feed. 

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

the top ten species by abundance and plotting the ln (abundance +1) against the rank of each 

species (Figure47). The plot for 2006 is indicative of a healthy benthic community with the top 

eight species having similar densities. If we examine similar plots for August of four years 

during our study (1977, 1989, 2002, and 2006), we can see that the shape of the curve has 

changed greatly between 1977 and 2006 (Figure48). The series of lines shows a community that 

was heavily dominated by three species in 1977 and 1989 when compared to the community in 

2002 when there was one dominant species. The 1977 community plot is the most extreme and 

reflects a bimodal species distribution with three species dominating the community and the 

remainder having similar but relatively low abundances. In contrast, the 2006 community plot 

has the flattest line (unimodal species distribution) which is indicative of a more evenly diverse 

community. 

It is informative to then examine these plots within the context of the life history 

characteristics of each species to determine if shifts in plot shape coincide with a shift in 

community structure and function that might be indicative of a healthier environment. We have 

shown two critical life history characteristics here: feeding mode (Figure48) and reproductive 

mode (Figure49). The 1977 community was dominated by filter-feeding species (species that 

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

feeding on the sediment surface (mixed feeders), and one species that feeds on food particles on 

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

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

sediment in their gut) dominated the community. In 2002 we again saw a shift towards species 

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

subsurface sediment. The most recent data shows that this homogenous community (the 

abundances are most similar between species) is mostly composed of a mix of subsurface deposit 

feeding species and mixed feeding species. Thus, over the period of this study we have seen a 

shift from a community dominated by species who fed either in the water column or on recently 

settled food particles on the sediment surface, to a community of species who feed directly on 

the subsurface sediment and those capable of feeding in the water column or on the sediment 

surface. 

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

for each point is equally informative (Figure49). The dominant species in 1977 were species 

that brood their young and release fully functional juveniles into the environment. In 1989 there 

were still several brooders but there were also two species that lay their eggs in the sediment. 

Although two brooding species remain in the ten most abundant species in the 2002 and 2006 

plots, the reproductive mode of the dominant species has shifted to those that spawn their 

gametes into the water column and those that lay eggs in the sediment (oviparous). It is possible 

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

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

depended on water borne larvae to repopulate the community. 
16

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; Cain and others 2006) with additional data from 

January 2006 through December 2006, to create a record spanning 33 years. This long-term 

dataset includes sediment chemistry, tissue concentrations of metals, condition index and 

reproductive activity in M. 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 (1970s) and the subsequent period when those concentrations 

declined. The sustained record of biogeochemical data at this site provides a rare opportunity to 

examine the biological response to metal contamination within this ecosystem. 

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

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

effluent being discharged from the PARWQCP to South Bay. In the early 1980s, the pointsource 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). Inter-annual trends in clams and sediments are 

highly correlated with copper loadings from PARWQCP. 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 (Hornberger and others, 2000b). 

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 M. petalum and sediment had just 

begun. 
17

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

biological responses to this metal decline. Reproductive activity improved within a year or two 

of reduced metal exposure, and responses at the population and community levels were observed 

afterward. Identification of these responses was possible because the frequency of sampling 

allowed long-term trends related to metal contamination to be identified within the context of 

repeating seasonal cycles and unrelated inter-annual variation. 

2004-2006 

Copper and Ag concentrations in sediments and the soft tissues of the clam M. petalum

during the three year period between 2004 and 2006 were representative of the concentrations 

observed since 1991 following significant reductions in concentrations during the 1980s that 

coincided with reductions in the discharge of these elements from PARWQCP. Since 1991, Cu 

and Ag concentrations in sediments and clams have remained relatively low and stable 

(compared to the late 1970s and the 1980s). Inter-annual variation during the 15 years since 

1991 did not correlate with discharge of Cu and Ag from PARWQCP, suggesting that, similar to 

other elements of regulatory interest including Cr, V, Ni, and Zn, regional scale factors now 

largely influence sedimentary and bioavailable concentrations (e.g. Luoma and others 1998). 

Other variables, such as precipitation and accelerated erosion of salt marsh banks in recent years, 

may influence the seasonal and year to year patterns in sedimentary and tissue concentrations 

and 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 M. petalum that has been sustained though 2006. The abundances of individual species 

showed no remarkable variability during 2004-2006. The species abundances of the 2006 

community were the most homogenous, that is the ten most abundant species had the most 

similar abundances we have observed during this long term study. 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. The community has shifted from 

being dominated by species that live on the surface, filter food out of the water column or 

consume particles on the sediment surface, and brood their young, to a community dominated by 

species that live on and below the surface, consume the sediment directly to harvest food 

particles, and spawn and lay eggs in the sediment. 

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, 
18

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. Nanotechnologies, 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. 
19

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23

Figures 
24

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'

Sand Point 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'

Sand Point

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. 
25

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

Monthly Precipitation

0

5

10

15

Figure 2. Precipitation 

Data from San Mateo gauge station from 1994 through 2006. Precipitation is in inches. 
26

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

Salinity (parts per thousand)

0

5

10

15

20

25

30

35

Figure 3. Water column salinity 

Data from Palo Alto site from 1994 through 2006. 
27

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

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 2006. 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. 
28

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

0

50

100

150

200

, V, and Ni in sediment ( g/g) Cr

Figure 5. Chromium, nickel and vanadium in sediments 

Data are for the period from 1994 through 2006. Concentrations of chromium (Cr) (), nickel (Ni) (z) and 

vanadium (V) (S) extracted by near-total digest. 
29

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

Cu in sediment ( g/g)

0

20

40

60

80

260

280

300

ERM=270 g/g

ERL=34 g/g

Figure 6. Copper in sediments 

Data are for the period from 1994 through 2006. Near-total (S) and partial-extractable (|) copper. 
30

 

1989-2006: 

r2 = 0.29 

1977-2006: 

r2 = 0.77 

p< 0.0001 

Figure 7. Correlation between copper effluent from PARWQP and copper concentrations in 

surface sediments 
31

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

Zn in sediment ( g/g)

0

50

100

150

200

400

450

500

ERM = 410 g/g

ERL = 150 g/g

Regional 

Background = 75 g/g

Figure 8. Zinc in sediments 

Data are for the period from 1994 through 2006. Near-total (z) and partial-extractable (|) zinc. 
32

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

Ag in sediment ( g/g)

0.0

0.2

0.4

0.6

0.8

1.0

3.0

3.5

4.0

ERM = 3.7 g/g

ERL = 1 g/g

Regional 

Background =

0.09 g/g

Figure 9. Silver in sediments 

Data are for the period from 1994 through 2006. Data represent partial-extractable silver (treatment with 0.6 N 

hydrochloric acid). 
33

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

0.0

0.2

0.4

0.6

0.8

1.0

& in sediment ( g/g) Hg Se 

Figure 10. Selenium and mercury in sediments 

Data are for the period from 1994 through 2006. Selenium (T); mercury (). 
34

Year

1970 1975 1980 1985 1990 1995 2000 2005

Cu in clam tissue ( g/g)

0

100

200

300

400

Figure 11. Annual mean copper in Macoma petalum

Data are for the period from 1977 through 2006. The error bars are the standard error of the mean (SEM). 
35

Year

1970 1975 1980 1985 1990 1995 2000 2005

Ag in clam tissue ( g/g)

0

50

100

150

Figure 12. Annual mean silver in Macoma petalum

Data are for the period from 1977 through 2006. The error bars are the standard error of the mean (SEM). 
36

1989-2006: 

r2 = 0.10 

1977-2006: 

r2 = 0.90 

p< 0.0001 

Figure 13. Correlation between copper loadings from the PARWQP and copper concentrations in 

Macoma petalum
37

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 

Cu in clam tissue ( g/g)

0

30

60

90

120

150

Figure 14. 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). 
38

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 

Ag in clam tissue ( g/g)

0

3

6

9

12

15

Figure 15. 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). 
39

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 

0

3

6

9

12

in clam tissue ( g/g) Cr 

Figure 16. 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). 
40

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 

Ni in clam tissue ( g/g)

0

3

6

9

12

Figure 17. 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). 
41

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 

Zn in clam tissue ( g/g)

0

100

200

300

400

500

600

700

Figure 18. 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). 
42

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 

0.0

0.2

0.4

0.6

0.8

1.0

in clam tissue ( g/g) Hg 

Figure 19. 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). 
43

Date

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 

0

2

4

6

8

10

in clam tissue ( g/g) Se 

Figure 20. 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). 
44

Date

1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 

Tissue weight in mg (25mm clam)

0

50

100

150

200

250

300

Figure 21. 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. 
45

Year

1975 1980 1985 1990 1995 2000 2005 

% Non-reproductive % Reproductive

-100

-50

0

50

100

Figure 22. Reproductive activity of Macoma petalum

Data are for the period from 1974 through 2006. 
46

Year

2000 2001 2002 2003 2004 2005 2006 2007 

% Non-reproductive % Reproductive

-100

-50

0

50

100

Figure 23. Reproductive activity of Macoma petalum 2000 through 2006. 
47

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Species / 54cm2

0

10

20

30

Figure 24. Total number of species present 

Data are for the period from 1974 through 2006. 
48

Date

1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

500

1000

1500

Figure 25. Total average number of individuals present 

Data are for the period from 1974 through 2006. 
49

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

20

40

60

80

Figure 26. Average abundance of Macoma petalum

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
50

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

10

20

30

40

Figure 27. Average abundance of Mya arenaria

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
51

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

500

1000

1500

2000

Figure 28. Average abundance of Gemma gemma

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
52

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

250

500

750

Figure 29. Average abundance of Ampelisca abdita

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
53

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

150

300

450

600

Figure 30. Average abundance of Streblospio benedicti

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
54

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

20

40

60

80

100

Figure 31. Average abundance of Grandiderella japonica

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
55

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

5

10

15

Figure 32. Average abundance of Neanthes succinea 

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
56

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

20

40

60

80

Figure 33. Average abundance of Heteromastus filiformis

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
57

Date

1970 1975 1980 1985 1990 1995 2000 2005 

Number of Individuals / 54cm2

0

200

400

600

800

Figure 34. Average abundance of Nippoleucon hinumensis 

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 
58

Number of Individuals / 54cm

2

0

20

40

60

80

Ag in clam tissue ( g/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 ( g/g)

0

100

200

300

400

500

600

Figure 35. Heteromastus filiformis abundance with silver and copper in Macoma petalum. 

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 

The number of individuals (z); tissue concentration of silver () and copper ({) in M. petalum.
59

Ag in clam tissue ( g/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 ( g/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 36. Heteromastus filiformis annual abundance with silver in M. petalum and 

sediment 

Data are for the period from 1974 through 2006. 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

Cu in clam tissue ( g/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 ( g/g)

0

30

60

90

120

Figure 37. Heteromastus filiformis annual abundance with copper in M. petalum and sediment 

Data are for the period from 1974 through 2006. 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). 
61

Number of Individuals / 54cm

2

0

250

500

750

Ag in clam tissue ( g/g)

0

50

100

150

200

250

Date

1970 1975 1980 1985 1990 1995 2000 2005 

0

250

500

750

Cu in clam tissue ( g/g)

0

100

200

300

400

500

600

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

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 

Number of individuals (z) with silver () and copper ({) tissue concentrations in Macoma petalum.
62

Ag in clam tissue ( g/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 ( g/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 39. Ampelisca abdita annual abundance with silver in M. petalum and sediment 

Data are for the period from 1974 through 2006. 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

Cu in clam tissue ( g/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 ( g/g)

0

30

60

90

120

Figure 40. Ampelisca abdita annual abundance with copper in M. petalum and sediment 

Data are for the period from 1974 through 2006. 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). 
64

Number of Individuals / 54cm

2

0

150

300

450

600

Ag in clam tissue ( g/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 ( g/g)

0

100

200

300

400

500

600

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

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 

Number of individuals (z) with silver () and copper ({) tissue concentrations in Macoma petalum.
65

Ag in clam tissue ( g/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 ( g/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 42. Streblospio benedicti annual abundance with silver in M. petalum and sediment. 

Data are for the period from 1974 through 2006. 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

Cu in clam tissue ( g/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 ( g/g)

0

30

60

90

120

Figure 43. Streblospio benedicti annual abundance with copper in M. petalum and sediment 

Data are for the period from 1974 through 2006. 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). 
67

Number of Individuals / 54cm

2

0

500

1000

1500

2000

Ag in clam tissue ( g/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 ( g/g)

0

100

200

300

400

500

600

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

Data are for the period from 1974 through 2006. Error bars represent standard deviation from 3 replicate samplings. 

Number of individuals (z) with silver () and copper ({) tissue concentrations in Macoma petalum.
68

Ag in clam tissue ( g/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 ( g/g)

0.0

0.5

1.0

1.5

2.0

2.5

Figure 45. Gemma gemma annual abundance with silver in M. petalum and sediment. 

Data are for the period from 1974 through 2006. 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). 
69

Cu in clam tissue ( g/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 ( g/g)

0

30

60

90

120

Figure 46. Gemma gemma annual abundance with copper in M. petalum and sediment 

Data are for the period from 1974 through 2006. 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). 
70

2006

Gemma gemma 

T ubificidae 

Heteromas tus filiformis

Macoma petalum 

Nippoleuc on hinumens is 

S treblos pio benedic ti 

Ampelis ca abdita 

Nematoda 

C orbula amurens is

C orophium alienens e

0

0.5

1

1.5

2

2.5

3

3.5

4

1 2 3 4 5 6 7 8 9 10

Rank

L n (Averag e +1)

Figure 47. Benthic community rank-abundance data for 2006. 

Species name for each rank is shown. 
71

F eeding Types

F ilter

S urface 

Depos it

F ilter 

Mixed

C arnivore

Mixed Depos it C arnivore

Mixed *

Mixed

Mixed

Depos it

F ilter

F ilter

Depos it C arnivore Depos it

F ilter

C arnivore

Mixed

F ilter

Mixed

Mixed

Depos it

Depos it

Mixed

C arnivore F ilter Mixed

Mixed

F ilter

Depos it

Depos it Mixed

Mixed

S urfac e 

Depos it F ilter S urface

Depos it

F ilter Mixed

0

1

2

3

4

5

6

7

1 2 3 4 5 6 7 8 910

Rank

L n (Averag e +1)

1977 1989 2002 2006

Figure 48. Benthic community rank-abundance data for 1977, 1989, 2002, and 2006. Feeding mode 

for each species at each rank is shown. 

(Filter: filters food particles from water column; Deposit: ingests subsurface sediment and 

removes food from sediment in gut; Surface Deposit: ingests food particles on surface 

sediment; Mixed: capable of filter feeding and surface deposit feeding: Carnivore: predator on 

other fauna). 
72

R eproduc tive T ypes

B rooder

B rooder

B rooder

B rooder

Oviparous

S pawner

Oviparous S pawner

B rooder

B rooder

B rooder

Oviparous

B rooder

B rooder

Oviparous

S pawner B rooder

S pawner

Oviparous

S pawner

B rooder

B rooder

Oviparous

Oviparous

S pawner

S pawner

S pawner S pawner B rooder

B rooder

B rooder

Oviparous

Oviparous S pawner

B rooder

B rooder

B rooder B rooder

S pawner B rooder

0

1

2

3

4

5

6

7

1 2 3 4 5 6 7 8 910

Rank

L n (Averag e + 1)

1977 1989 2002 2006

Figure 49. Benthic community rank-abundance data for 1977, 1989, 2002, and 2006. 

Reproductive mode for each species at each rank is shown (Brooder: broods young and release 

juveniles as fully functional “miniature adults”; Oviparous: lays eggs in or on sediment; 

Spawner: releases gametes into water column and juveniles settle out of plankton onto sediment 

surface after growth in the plankton). 
73

Tables 
74

Table 1. Sediment characteristics and salinity in 2006 

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). 

[Units are microgram per gram dry weight. STD is standard deviation of the two samples. SEM is standard error of the means for the year.] 

Date Al Fe TOC Sand Salinity 

 (percent) (percent) (percent) (percent) (ppt) 

 mean std mean std 

January 9, 2006 5.6 0.2 4.5 0.1 1.5 26 18 

February 7, 2006 5.4 0.3 4.2 0.0 1.4 14 12 

March 22, 2006 4.8 0.1 3.9 0.1 1.2 33 13 

April 24, 2006 5.3 0.5 4.2 0.1 1.3 13 8 

May 31, 2006 5.0 0.0 3.9 0.1 1.1 65 10 

June 27, 2006 3.9 0.1 3.3 0.0 1.0 33 15 

September 7, 2006 4.7 0.2 4.0 0.0 1.1 24 21 

October 19, 2006 4.5 0.3 4.2 0.2 1.1 16 25 

December 18, 2006 4.6 0.1 4.1 0.0 1.1 37 24 

Annual Mean: 4.9 4.0 1.20 29 16 

SEM: 0.2 0.1 0.06 5 2 
75

Table 2. Concentrations of trace elements in sediments in 2006 

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). 

[Units are microgram per gram dry weight. STD is standard deviation of the two samples. SEM is standard error of the means for the year.] 

Date Ag Cr Cu Hg Ni Se V Zn 

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

January 9, 2006 0.33 0.00 130 3 55 2 0.2 96 2 0.8 115 3 310 223 

February 7, 2006 0.36 0.00 131 6 50 0 0.2 93 1 0.6 98 3 140 1 

March 22, 2006 0.33 0.00 120 4 48 1 - 89 1 - 96 10 121 9 

April 24, 2006 0.29 0.00 126 9 49 1 0.3 93 0 0.6 103 8 138 0 

May 31, 2006 0.45 0.00 117 0 47 1 - 83 1 - 97 11 115 7 

June 27, 2006 0.33 0.03 100 4 37 0 0.2 68 1 0.4 90 3 90 1 

September 7, 2006 0.39 0.01 118 7 44 1 0.2 87 1 0.4 95 2 123 2 

October 19, 2006 0.39 0.01 119 8 43 2 - 96 3 - 93 7 131 7 

December 18, 2006 0.36 0.00 123 1 42 0 0.3 89 1 0.4 92 1 125 1 

Annual Mean: 0.36 120 46 0.2 88 0.5 98 144 

SEM: 0.02 3 2 0.0 3 0.1 2 21 
76

Table 3. Annual mean copper in Macoma petalum and sediments 1977 through 2006 

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. HCl refers to hydrochloric acid extractable copper. 

Copper in sediment Copper 

Year HCl Total in clams 

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 

2006 18±2 46±2 45±8 
77

Table 4. Annual mean silver in Macoma petalum and sediments 1977 through 2006 

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. Sediment was extracted with 0.6 N hydrochloric acid. ND refers to No Data. 

Silver in Silver in 

Year sediment clams 

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 ± 0.03 2.1 ± 0.5 

2004 0.29 ± 0.06 2.4 ± 1.3 

2005 0.41 ± 0.04 1.8 ± 0.3 

2006 0.36 ± 0.05 3.8 ± 0.8 
78

Table 5. Concentrations of trace elements in Macoma petalum in 2006. 

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 (CI) is the soft tissue weight in milligrams of a 25 mm shell length clam. 

Date Ag Cr Cu Hg Ni Se Zn Condition Index

January 9, 2006 mean 2.9 3.5 29 - 5.7 - 358 83

*SEM 0.3 0.2 1 - 0.2 - 22

February 7, 2006 mean 2.5 5.5 28 0.31 6.8 6.47 438 81

*SEM 0.2 0.8 2 0.02 0.5 0.14 26

March 22, 2006 mean 1.2 2.9 19 - 4.4 - 311 125

*SEM 0.1 0.4 1 - 0.4 - 15

April 24, 2006 mean 1.3 1.5 23 0.16 3.5 4.80 331 123

*SEM 0.1 0.1 1 0.02 0.2 0.04 7

May 31, 2006 mean 2.1 1.5 34 - 4.1 - 417 102

*SEM 0.4 0.3 6 - 0.8 - 87

June 27, 2006 mean 3.7 2.3 54 0.27 5.9 4.17 442 95

*SEM 0.3 0.2 3 0.02 0.5 0.04 36

September 7, 2006 mean 4.6 2.3 66 0.37 6.2 4.47 383 75

*SEM 0.3 0.1 3 0.03 0.2 0.03 29

October 19, 2006 mean 7.9 3.5 83 - 7.6 - 425 81

*SEM 0.9 0.4 5 - 0.6 - 32

December 18, 2006 mean 7.6 4.6 67 0.49 7.9 6.27 446 89

*SEM 0.4 0.1 3 0.02 0.2 0.13 19

Annual Mean: 3.8 3.1 45 0.32 5.8 5.2 395 95

SEM: 0.8 0.5 8 0.05 0.5 0.5 17 6

[All units microgram per gram soft tissue dry weight. Wt.25mm is the condition index or weight in milligrams of a 

25 mm shell length clam. *SEM is standard errors of the means from 6-14 replicate analyses of composite 

samples.] 
79

Appendix A 

Sediment characteristics for samples collected between 1994 and 2006. 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. 
80

PALTO ALTO GRAIN SIZE DATA: <100μm 

Year Date %<100μm Year Date %<100μm Year Date %<100μm

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 10/01/05 50 

 12/05/95 76 2001 01/09/01 59 12/13/05 79 

1996 01/17/96 85 02/05/01 68 2006 01/09/06 74 

 02/13/96 96 03/05/01 71 02/07/06 86 

 03/13/96 98 04/10/01 88 03/22/06 67 

 04/10/96 86 05/08/01 79 04/24/06 87 

 06/18/96 79 06/12/01 61 05/31/06 35 

 09/26/96 84 09/18/01 41 06/27/06 67 

 12/09/96 70 10/15/01 61 09/07/06 76 

1997 01/08/97 75 12/11/01 84 10/19/06 84 

 02/19/97 92 2002 01/08/02 55 12/18/06 63 

 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 
81

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 2007 

Percent silt/clay ( uM)

20

40

60

80

100

120
82

A-3. Total organic carbon (TOC) content (expressed as percent) of sediment collected in 2006. 

Date of collection TOC (%) 

January 9, 2006 1.52 

February 7, 2006 1.42 

March 22, 2006 1.17 

April 24, 2006 1.33 

May 31, 2006 1.13 

June 27, 2006 0.97 

September 7, 2006 1.11 

October 19, 2006 1.09 

December 18, 2006 1.10 
Appendix B 

Metal concentrations in sediments collected at the Palo Alto mudflat during 2006 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 standarare reported, also. Note: Appendix tables in this document may not be 508 complaint. 508 compliant Excel spreadsheet containing these 

may be accessed at URL: http://pubs.usgs.gov/of/2007/1199/Appendix-B.xls 

83
Palo Alto Total Extracts: 2006

1/09/2006: 74% <100 μm

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.5012 10 10 287.90 0.66 0.27 222.40 4.17 0.47 0.2Tot2 0.4973 10 10 273.60 0.64 0.28 227.00 4.31 0.48 0.2

Average 56229.62 130.31 55.34 45010.00 849.24 95.74 44.5

Std 1714.77 3.19 1.59 900.14 25.51 2.10 1.1

2/07/2006: 86% < 100 μm

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB 

Tot1 0.5005 10 10 281.1 0.6744 0.2492 208.7 4.823 0.4638 0.21Tot2 0.5178 10 10 271.7 0.6563 0.2598 216.2 5.021 0.4849 0.21

Average 54317.92 130.75 49.98 41725.94 966.66 93.16 42.1

Std 2610.52 5.66 0.27 39.08 4.27 0.69 1.6

3/22/2006: 67% <100 μmSample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB Tot1 0.5152 10 10 243.5 0.6314 0.244 199 3.956 0.4594 0.18Tot2 0.5337 10 10 259.4 0.6234 0.2596 213.8 4.351 0.47 0.18

Average 47933.64 119.68 48.00 39342.87 791.55 88.62 36.1

Std 948.15 4.06 0.91 1014.12 33.51 0.78 1.0

4/24/2006: 87% <100 μmSample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB Tot1 0.5414 10 10 267.1 0.6456 0.2622 226 4.727 0.5034 0.20Tot2 0.4941 10 10 278.8 0.6538 0.2437 212.4 4.394 0.4604 0.20

Average 52880.44 125.78 48.88 42365.44 881.20 93.08 40.5

Std 5013.93 9.25 0.63 879.37 11.45 0.14 2.7

84
85

5/31/2006: 35% < 100 μmSample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB Tot1 0.4889 10 10 243.9 0.5728 0.2262 188.2 3.785 0.4051 0.1705 Tot2 0.4684 10 10 236.7 0.5481 0.2235 184.7 3.68 0.3915 0.1632 

Average 50210.62 117.09 46.99 38963.34 779.92 83.22 34.86 

Std 456.95 0.10 1.02 662.93 8.11 0.51 0.02 

6/27/2006: 67% <100 μmSample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB Tot1 0.5341 10 10 204.8 0.5211 0.1982 175.2 3.393 0.3635 0.1676 Tot2 0.5115 10 10 205 0.5273 0.1927 171.4 3.33 0.352 0.1625 

Average 39211.54 100.33 37.39 33156.07 643.15 68.44 31.57 

Std 1225.64 3.91 0.40 499.53 11.14 0.54 0.28 

9/7/2006: 76% <100 μmSample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB Tot1 0.4867 10 10 225.6 0.5497 0.209 196.2 4.932 0.4175 0.2133 Tot2 0.4882 10 10 236.8 0.602 0.2181 193.9 4.59 0.4273 0.254 

Average 47428.85 118.13 43.81 40014.82 976.77 86.65 47.93 

Std 1521.50 7.33 1.22 420.71 51.74 1.23 5.80 

10/19/2006: 84% <100 μmSample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB Tot1 0.4816 10 10 205.4 0.5427 0.2008 196.9 5.208 0.4499 0.2485 Tot2 0.5183 10 10 245.8 0.645 0.2339 223.3 5.789 0.5084 0.2817 

Average 45036.89 118.57 43.41 41983.85 1099.16 95.75 52.97 

Std 3376.27 8.31 2.43 1554.65 25.12 3.30 1.95 
12/18/2006: 63% <100 μm

Sample Weight (g) Recon. (ml) Dil. Factor AL CR CU FE MN NI PB Tot1 0.5504 10 10 250.2 0.6826 0.232 225.1 5.779 0.4975 0.2856 Tot2 0.5039 10 10 238.4 0.6173 0.2157 206.5 5.286 0.445 0.2569 

Average 46384.41 123.26 42.48 40938.94 1049.49 89.35 51.44 

Std 1310.36 1.07 0.46 58.57 0.67 1.47 0.64 

Palo Alto HCl Extracts: 20061/09/2006: 74% <100 μmSample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PB HCl1 0.519 10 0.017 88.21 0.2162 1.089 232.7 21.67 0.5856 0.97HCL2 0.5065 10 0.0168 85.21 0.205 1.064 223.8 21.11 0.5602 0.94

Average 0.33 1690.97 4.11 20.99 4451.09 417.16 11.17 18.7Std 0.00 8.64 0.06 0.01 32.53 0.38 0.11 0.0

2/07/2006: 86% < 100 μmSample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PB HCl1 0.5 10 0.0181 83.13 0.2294 1.007 237.8 25.58 0.5417 0.99

HCL2 0.5053 10 0.018 80.26 0.2147 0.9973 231 25.53 0.5137 0.99

Average 0.36 1625.48 4.42 19.94 4663.77 508.42 10.50 19.8Std 0.00 37.12 0.17 0.20 92.23 3.18 0.33 0.1

86
3/22/2006: 67% <100 μm

Sample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PHCl1 0.4937 10 0.0164 73.12 0.2065 0.9257 197.6 17.65 0.4839 0.

HCL2 0.5066 10 0.0167 76.49 0.2206 0.9675 209.1 18.55 0.5229 0.

Average 0.33 1495.47 4.27 18.92 4064.97 361.84 10.06 1Std 0.00 14.40 0.09 0.17 62.54 4.33 0.26 0

4/24/2006: 87% <100 μmSample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PHCl1 0.5168 10 0.0149 84.13 0.2266 0.9961 246.1 22.54 0.568 1

HCL2 0.6545 10 0.0194 103.9 0.2792 1.255 295.2 27.94 0.6967 1

Average 0.29 1607.69 4.33 19.22 4636.16 431.52 10.82 1Std 0.00 20.22 0.06 0.05 125.84 4.63 0.17 0

5/31/2006: 35% < 100 μmSample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PHCl1 0.3516 10 0.0159 47.29 0.1197 0.5967 121.3 12.25 0.3118 0

HCL2 0.3412 10 0.0152 45.77 0.1195 0.5708 117.9 12.05 0.3052 0.

Average 0.45 1343.22 3.45 16.85 3452.70 350.79 8.91 1Std 0.00 1.78 0.05 0.12 2.75 2.38 0.04 0

6/27/2006: 67% <100 μmSample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PHCl1 0.6779 10 0.0206 98.9 0.2379 1.009 258.5 21.16 0.4342 0.

HCl2 0.5012 10 0.0178 75.45 0.1846 0.7587 201.9 16.58 0.3379 0.

Average 0.33 1482.15 3.60 15.01 3920.79 321.47 6.57 1Std 0.03 23.23 0.09 0.13 107.54 9.33 0.17 0

87
88

9/7/2006: 76% <100 μmSample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PB HCl1 0.4869 10 0.0188 85.34 0.2096 0.7891 201.2 24.91 0.3476 0.84HCl2 0.4359 10 0.0174 77.81 0.1912 0.7125 186.3 22.52 0.3202 0.75

Average 0.39 1768.88 4.35 16.28 4203.09 514.12 7.24 17.4Std 0.01 16.16 0.04 0.07 70.83 2.51 0.10 0.0

10/19/2006: 84% <100 μmSample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PB HCl1 0.4432 10 0.0181 78.41 0.1927 0.7097 194.4 26.12 0.3111 0.76

HCl2 0.5163 10 0.0197 90.82 0.2253 0.828 222.8 30.23 0.3602 0.88

Average 0.39 1764.12 4.36 16.03 4350.80 587.43 7.00 17.1Std 0.01 5.06 0.01 0.01 35.48 1.92 0.02 0.0

12/18/2006: 63% <100 μmSample Weight (g) Recon. (ml) Ag AL CR CU FE MN NI PB HCl1 0.432 10 0.0157 78.08 0.2022 0.705 195.4 25.32 0.3231 0.74

HCl2 0.4514 10 0.0165 81.42 0.2079 0.7315 203.9 26.36 0.3325 0.82

Average 0.36 1805.56 4.64 16.26 4520.10 585.04 7.42 17.8Std 0.00 1.84 0.04 0.06 3.05 1.08 0.06 0.4
89

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. 

Note: Appendix tables in this document may not be 508 complaint. 508 compliant Excel spreadsheet 

containing these 508 compliant tables may be accessed at URL: 

http://pubs.usgs.gov/of/2007/1199/Appendix-C.xls 
90

Station: Statistical Summary

Date:PA 01/09/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 2.8647 0.1328 3.4933 28.7805 5.7090 1.5238 4.1409 358.0370

STD 0.8272 0.0622 0.5905 2.4894 0.5895 0.2911 0.7834 70.6395

SEM 0.262 0.022 0.187 0.787 0.186 0.092 0.248 22.338

CV% 28.876 46.846 16.904 8.650 10.326 19.104 18.918 19.730

n 10 8 10 10 10 10 10 10

r wt x [ ] 0.250 0.383 0.211 0.626 0.380 0.128 0.339 0.438

X 100mg 3.686 0.044 2.999 34.956 4.821 1.376 3.087 235.450

r l x [ ] 0.300 0.341 0.239 0.628 0.381 0.105 0.379 0.483

X 20mm 3.072 0.119 3.375 30.084 5.522 1.498 3.893 329.574

X 25mm 3.392 0.091 3.193 32.102 5.232 1.459 3.509 285.499

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.1330 0.0046 0.1491 1.3468 0.2470 0.0662 0.1727 14.3565

25mm 0.2656 0.0072 0.2651 2.6228 0.4417 0.1206 0.2998 23.9782

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.020 gm 0.045 gm

20.265 mg 44.935 mg

Estimated weight for 25mm clam

0.083 gm

83.336 mg
Station: Palo Alto Macoma petalum

Date:01/09/06

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

Mp1 11.42 0.0896 0.0090 10 0.0219 -0.0005 0.0366 0.2524 0.0574 0.0153 0.0489 3.817

Mp2 12.52 0.1892 0.0118 10 0.0532 0.0036 0.0775 0.5478 0.1192 0.0368 0.0958 7.876

Mp3 13.44 0.1675 0.0152 10 0.0319 0.0015 0.051 0.426 0.0827 0.02 0.0567 6.421

Mp4 14.31 0.2322 0.0166 10 0.0706 0.0045 0.0806 0.6211 0.1384 0.0371 0.0886 8.967

Mp5 15.60 0.1107 0.0277 10 0.0295 -0.0007 0.0318 0.2808 0.0575 0.0109 0.0379 4

Mp6 17.47 0.1333 0.0333 10 0.0313 0.0008 0.0592 0.3981 0.0878 0.0238 0.068 3.253

Mp7 18.84 0.3011 0.0376 10 0.1285 0.0056 0.0785 0.9727 0.1591 0.0409 0.1023 10.33

Mp8 20.44 0.3239 0.0463 10 0.1404 0.0062 0.1014 0.9137 0.1891 0.0546 0.1179 10.74

Mp9 21.48 0.1647 0.0549 10 0.0448 0.0014 0.0585 0.5282 0.0898 0.0228 0.068 7.364

Mp10 22.18 0.1649 0.0550 10 0.0348 0.0011 0.0599 0.506 0.0846 0.0263 0.0659 3.981

MDL 0.0010 0.0004 0.0026 0.0011 0.0010 0.0033 0.0012 0.0037

MRL 0.0020 0.0008 0.0052 0.0021 0.0019 0.0066 0.0024 0.0073

Sample #

 Concentration (ug/g) ==> Mp1 2.4442 4.0848 28.1696 6.4063 1.7076 5.4576 426.004

Mp2 2.8118 0.1903 4.0962 28.9535 6.3002 1.9450 5.0634 416.279

Mp3 1.9045 0.0896 3.0448 25.4328 4.9373 1.1940 3.3851 383.343

Mp4 3.0405 0.1938 3.4711 26.7485 5.9604 1.5978 3.8157 386.176

Mp5 2.6649 2.8726 25.3659 5.1942 0.9846 3.4237 361.337

Mp6 2.3481 0.0600 4.4411 29.8650 6.5866 1.7854 5.1013 244.036

Mp7 4.2677 0.1860 2.6071 32.3049 5.2840 1.3584 3.3975 343.075

Mp8 4.3347 0.1914 3.1306 28.2093 5.8382 1.6857 3.6400 331.584

Mp9 2.7201 0.0850 3.5519 32.0704 5.4523 1.3843 4.1287 447.116

Mp10 2.1104 0.0667 3.6325 30.6853 5.1304 1.5949 3.9964 241.419

Sample #

 Content (ug) ==> Mp1 0.0219 0.0366 0.2524 0.0574 0.0153 0.0489 3.8170

Mp2 0.0333 0.0023 0.0484 0.3424 0.0745 0.0230 0.0599 4.9225

Mp3 0.0290 0.0014 0.0464 0.3873 0.0752 0.0182 0.0515 5.8373

Mp4 0.0504 0.0032 0.0576 0.4436 0.0989 0.0265 0.0633 6.4050

Mp5 0.0738 0.0795 0.7020 0.1438 0.0273 0.0948 10.0000

Mp6 0.0783 0.0020 0.1480 0.9953 0.2195 0.0595 0.1700 8.1325

Mp7 0.1606 0.0070 0.0981 1.2159 0.1989 0.0511 0.1279 12.9125

Mp8 0.2006 0.0089 0.1449 1.3053 0.2701 0.0780 0.1684 15.3429

Mp9 0.1493 0.0047 0.1950 1.7607 0.2993 0.0760 0.2267 24.5467

Mp10 0.1160 0.0037 0.1997 1.6867 0.2820 0.0877 0.2197 13.2700

91
Station: Palo Alto Statistical Summary

Date: 02/07/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 2.5395 0.2287 5.5210 27.5377 6.8229 1.6795 5.9233 437.7184

STD 0.5571 0.1151 2.3494 6.4175 1.5739 0.5889 2.3039 76.9485

SEM 0.186 0.047 0.783 2.139 0.525 0.196 0.768 25.649

CV% 21.938 50.351 42.554 23.304 23.068 35.062 38.895 17.579

n 96999999

r wt x [ ] 0.758 0.332 0.171 0.561 0.308 0.333 0.289 0.712

X 100mg 4.397 0.077 7.283 43.360 8.952 2.541 8.855 678.827

r l x [ ] 0.736 0.256 0.132 0.549 0.308 0.372 0.268 0.775

X 20mm 3.019 0.203 5.885 31.660 7.390 1.936 6.644 507.424

X 25mm 3.539 0.164 6.279 36.125 8.004 2.213 7.425 582.941

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.1405 0.0081 0.2416 1.4531 0.3280 0.0814 0.2736 23.7285

25mm 0.2807 0.0124 0.4228 2.8016 0.5909 0.1527 0.4954 46.4138

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.023 gm 0.047 gm

23.100 mg 46.873 mg

Estimated weight for 25mm clam

0.081 gm

81.149 mg

92
Station: Palo Alto Macoma petalum

Date: 02/07/06

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

Mp1 10.04 0.0275 0.0092 10 0.006 -0.0027 0.0249 0.0724 0.0221 0.0045 0.0231 0.8495

Mp2 11.65 0.1000 0.0125 10 0.0169 -0.0001 0.038 0.1971 0.0566 0.0113 0.0399 3.994

Mp3 12.43 0.1330 0.0148 10 0.0296 0.0022 0.058 0.302 0.0825 0.0259 0.0678 5.46

Mp4 13.49 0.2699 0.0142 10 0.0658 0.0109 0.154 0.7219 0.1917 0.0547 0.1687 13.62

Mp5 14.55 0.2105 0.0211 10 0.0455 0.0056 0.0937 0.4877 0.1301 0.0269 0.0987 7.767

Mp6 16.32 0.1339 0.0335 10 0.0437 -0.0007 0.0306 0.398 0.0518 0.0083 0.0332 6.032

Mp7 18.70 0.0829 0.0415 10 0.0274 0.0006 0.053 0.3373 0.073 0.0201 0.0629 3.592

Mp8 19.64 0.1344 0.0448 10 0.034 0.0024 0.0593 0.4544 0.0923 0.023 0.0677 6.771

Mp9 21.64 0.1085 0.0543 10 0.0332 0.0031 0.1001 0.2708 0.0942 0.0254 0.1061 6.07

MDL 0.0010 0.0004 0.0026 0.0011 0.0010 0.0033 0.0012 0.0037

MRL 0.0020 0.0008 0.0052 0.0021 0.0019 0.0066 0.0024 0.0073

Sample #

 Concentration (ug/g) ==> Mp1 2.1818 9.0545 26.3273 8.0364 1.6364 8.4000 308.909

Mp2 1.6900 3.8000 19.7100 5.6600 1.1300 3.9900 399.400

Mp3 2.2256 0.1654 4.3609 22.7068 6.2030 1.9474 5.0977 410.526

Mp4 2.4379 0.4039 5.7058 26.7469 7.1026 2.0267 6.2505 504.631

Mp5 2.1615 0.2660 4.4513 23.1686 6.1805 1.2779 4.6888 368.979

Mp6 3.2636 2.2853 29.7237 3.8686 0.6199 2.4795 450.485

Mp7 3.3052 0.0724 6.3932 40.6876 8.8058 2.4246 7.5875 433.293

Mp8 2.5298 0.1786 4.4122 33.8095 6.8676 1.7113 5.0372 503.795

Mp9 3.0599 0.2857 9.2258 24.9585 8.6820 2.3410 9.7788 559.447

Sample #

 Content (ug) ==> Mp1 0.0200 0.0830 0.2413 0.0737 0.0150 0.0770 2.8317

Mp2 0.0211 0.0475 0.2464 0.0708 0.0141 0.0499 4.9925

Mp3 0.0329 0.0024 0.0644 0.3356 0.0917 0.0288 0.0753 6.0667

Mp4 0.0346 0.0057 0.0811 0.3799 0.1009 0.0288 0.0888 7.1684

Mp5 0.0455 0.0056 0.0937 0.4877 0.1301 0.0269 0.0987 7.7670

Mp6 0.1093 0.0765 0.9950 0.1295 0.0208 0.0830 15.0800

Mp7 0.1370 0.0030 0.2650 1.6865 0.3650 0.1005 0.3145 17.9600

Mp8 0.1133 0.0080 0.1977 1.5147 0.3077 0.0767 0.2257 22.5700

Mp9 0.1660 0.0155 0.5005 1.3540 0.4710 0.1270 0.5305 30.3500

93
Station: Palo Alto Statistical Summary

Date: 03/22/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 1.2244 0.1847 2.8586 19.4769 4.4335 1.1223 3.0644 310.6788

STD 0.4249 0.0649 1.1133 3.3543 1.1864 0.4375 1.2874 45.8747

SEM 0.134 0.023 0.352 1.061 0.375 0.138 0.407 14.507

CV% 34.700 35.124 38.945 17.222 26.760 38.985 42.011 14.766

n 10 8 10 10 10 10 10 10

r wt x [ ] 0.504 0.489 0.200 0.556 0.320 0.307 0.325 0.700

X 100mg 1.591 0.251 3.239 22.670 5.083 1.352 3.780 365.658

r l x [ ] 0.627 0.536 0.368 0.693 0.495 0.480 0.486 0.752

X 20mm 1.424 0.214 3.166 21.222 4.874 1.280 3.534 336.596

X 25mm 1.786 0.270 3.722 24.377 5.671 1.565 4.382 383.431

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.0924 0.0137 0.1968 1.4344 0.3227 0.0823 0.2239 22.9514

25mm 0.2046 0.0320 0.4044 2.9544 0.6717 0.1833 0.5042 47.3113

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.031 gm 0.068 gm

31.253 mg 68.176 mg

Estimated weight for 25mm clam

0.125 gm

124.845 mg

94
Station: Palo Alto Macoma petalum

Date: 03/22/06

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

Mp1 11.49 0.1440 0.0160 10 0.0116 -0.0006 0.0264 0.2332 0.0473 0.0086 0.0276 3.42

Mp2 13.53 0.1661 0.0237 10 0.0186 0.0016 0.0285 0.246 0.0532 0.0108 0.022 4.365

Mp3 14.46 0.3592 0.0276 10 0.0426 0.0066 0.1279 0.6737 0.1716 0.0502 0.1354 11.17

Mp4 15.39 0.5573 0.0348 15 0.0326 0.0064 0.0974 0.7197 0.1463 0.0377 0.0949 10.85

Mp5 16.46 0.4968 0.0355 10 0.0627 0.0134 0.1829 1.077 0.2458 0.0639 0.1929 17.19

Mp6 17.51 0.4915 0.0492 10 0.0477 0.0081 0.117 0.8895 0.1784 0.0446 0.1224 15.54

Mp7 18.36 0.1891 0.0473 10 0.0265 0.0022 0.0618 0.384 0.1103 0.0285 0.0729 5.221

Mp8 20.61 0.3349 0.0837 10 0.0442 0.0065 0.1186 0.6439 0.1743 0.0484 0.1312 12.77

Mp9 21.82 0.1940 0.0970 10 0.0194 -0.0001 0.0226 0.37 0.0593 0.0112 0.0306 6.098

Mp10 22.71 0.2642 0.0881 10 0.0608 0.0074 0.1273 0.7201 0.1707 0.0486 0.1415 9.764

MDL 0.0010 0.0004 0.0026 0.0011 0.0010 0.0033 0.0012 0.0037

MRL 0.0020 0.0008 0.0052 0.0021 0.0019 0.0066 0.0024 0.0073

Sample #

 Concentration (ug/g) ==> Mp1 0.8056 1.8333 16.1944 3.2847 0.5972 1.9167 237.500

Mp2 1.1198 0.0963 1.7158 14.8104 3.2029 0.6502 1.3245 262.793

Mp3 1.1860 0.1837 3.5607 18.7556 4.7773 1.3976 3.7695 310.969

Mp4 0.8774 0.1723 2.6216 19.3711 3.9377 1.0147 2.5543 292.033

Mp5 1.2621 0.2697 3.6816 21.6787 4.9477 1.2862 3.8829 346.014

Mp6 0.9705 0.1648 2.3805 18.0977 3.6297 0.9074 2.4903 316.175

Mp7 1.4014 0.1163 3.2681 20.3067 5.8329 1.5071 3.8551 276.097

Mp8 1.3198 0.1941 3.5414 19.2266 5.2045 1.4452 3.9176 381.308

Mp9 1.0000 1.1649 19.0722 3.0567 0.5773 1.5773 314.330

Mp10 2.3013 0.2801 4.8183 27.2559 6.4610 1.8395 5.3558 369.569

Sample #

 Content (ug) ==> Mp1 0.0129 0.0293 0.2591 0.0526 0.0096 0.0307 3.8000

Mp2 0.0266 0.0023 0.0407 0.3514 0.0760 0.0154 0.0314 6.2357

Mp3 0.0328 0.0051 0.0984 0.5182 0.1320 0.0386 0.1042 8.5923

Mp4 0.0306 0.0060 0.0913 0.6747 0.1372 0.0353 0.0890 10.1719

Mp5 0.0448 0.0096 0.1306 0.7693 0.1756 0.0456 0.1378 12.2786

Mp6 0.0477 0.0081 0.1170 0.8895 0.1784 0.0446 0.1224 15.5400

Mp7 0.0663 0.0055 0.1545 0.9600 0.2758 0.0713 0.1823 13.0525

Mp8 0.1105 0.0163 0.2965 1.6098 0.4358 0.1210 0.3280 31.9250

Mp9 0.0970 0.1130 1.8500 0.2965 0.0560 0.1530 30.4900

Mp10 0.2027 0.0247 0.4243 2.4003 0.5690 0.1620 0.4717 32.5467

95
96

10

Station: Palo Alto Statistical Summary

Date: 04/24/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 1.3328 0.1966 1.4754 23.2069 3.5382 0.4625 1.3560 330.6337

STD 0.2807 0.0562 0.3739 3.4620 0.6275 0.2178 0.4236 22.8440

SEM 0.089 0.018 0.118 1.095 0.198 0.069 0.134 7.224

CV% 21.065 28.601 25.339 14.918 17.736 47.098 31.239 6.909

n 10 10 10 10 10 10 10

r wt x [ ] 0.237 0.114 0.371 0.644 0.619 0.561 0.122 0.197

X 100mg 1.296 0.200 1.399 21.976 3.753 0.530 1.327 328.152

r l x [ ] 0.060 0.323 0.302 0.560 0.615 0.583 0.060 0.121

X 20mm 1.331 0.198 1.465 23.026 3.574 0.474 1.354 330.377

X 25mm 1.313 0.218 1.344 20.947 3.988 0.610 1.326 327.421

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.0844 0.0125 0.0915 1.4606 0.2306 0.0290 0.0843 21.3505

25mm 0.1578 0.0288 0.1592 2.5373 0.4813 0.0692 0.1564 40.2691

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.028 gm 0.065 gm

28.383 mg 64.790 mg

Estimated weight for 25mm clam

0.123 gm

122.900 mg
Station: Palo Alto Macoma petalum

Date: 04/24/06

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

Mp1 13.41 0.1033 0.0207 10 0.0119 0.0007 0.0157 0.2716 0.0341 0.0038 0.0153 3.319

Mp2 15.45 0.1719 0.0344 10 0.0233 0.0027 0.028 0.3991 0.059 0.0047 0.0192 6.141

Mp3 16.44 0.3050 0.0339 10 0.0385 0.0071 0.0539 0.7551 0.1017 0.0162 0.0532 10.35

Mp4 17.53 0.5489 0.0422 15 0.0421 0.0074 0.043 0.7472 0.1112 0.0117 0.0376 10.92

Mp5 18.47 0.3629 0.0518 10 0.047 0.0079 0.0448 0.7663 0.0997 0.0123 0.0365 10.98

Mp6 19.20 0.2385 0.0596 10 0.0282 0.0046 0.0345 0.5535 0.0707 0.0076 0.0289 7.82

Mp7 20.33 0.2647 0.0662 10 0.0423 0.0069 0.0348 0.7302 0.12 0.0106 0.0362 9.326

Mp8 21.63 0.2368 0.0789 10 0.0434 0.0061 0.0551 0.6348 0.0964 0.0221 0.0561 8.504

Mp9 23.30 0.2051 0.1026 10 0.0333 0.0042 0.0276 0.464 0.0707 0.0078 0.0227 7.009

Mp10 29.91 0.2090 0.2090 10 0.0183 0.0036 0.0208 0.3353 0.0943 0.0159 0.0236 6.404

MDL 0.0010 0.0004 0.0026 0.0011 0.0010 0.0033 0.0012 0.0037

MRL 0.0020 0.0008 0.0052 0.0021 0.0019 0.0066 0.0024 0.0073

Sample #

 Concentration (ug/g) ==> Mp1 1.1520 0.0678 1.5198 26.2924 3.3011 0.3679 1.4811 321.297

Mp2 1.3554 0.1571 1.6289 23.2170 3.4322 0.2734 1.1169 357.243

Mp3 1.2623 0.2328 1.7672 24.7574 3.3344 0.5311 1.7443 339.344

Mp4 1.1505 0.2022 1.1751 20.4190 3.0388 0.3197 1.0275 298.415

Mp5 1.2951 0.2177 1.2345 21.1160 2.7473 0.3389 1.0058 302.563

Mp6 1.1824 0.1929 1.4465 23.2075 2.9644 0.3187 1.2117 327.883

Mp7 1.5980 0.2607 1.3147 27.5859 4.5334 0.4005 1.3676 352.323

Mp8 1.8328 0.2576 2.3269 26.8074 4.0709 0.9333 2.3691 359.122

Mp9 1.6236 0.2048 1.3457 22.6231 3.4471 0.3803 1.1068 341.736

Mp10 0.8756 0.1722 0.9952 16.0431 4.5120 0.7608 1.1292 306.411

Sample #

 Content (ug) ==> Mp1 0.0238 0.0014 0.0314 0.5432 0.0682 0.0076 0.0306 6.6380

Mp2 0.0466 0.0054 0.0560 0.7982 0.1180 0.0094 0.0384 12.2820

Mp3 0.0428 0.0079 0.0599 0.8390 0.1130 0.0180 0.0591 11.5000

Mp4 0.0486 0.0085 0.0496 0.8622 0.1283 0.0135 0.0434 12.6000

Mp5 0.0671 0.0113 0.0640 1.0947 0.1424 0.0176 0.0521 15.6857

Mp6 0.0705 0.0115 0.0863 1.3838 0.1768 0.0190 0.0723 19.5500

Mp7 0.1058 0.0173 0.0870 1.8255 0.3000 0.0265 0.0905 23.3150

Mp8 0.1447 0.0203 0.1837 2.1160 0.3213 0.0737 0.1870 28.3467

Mp9 0.1665 0.0210 0.1380 2.3200 0.3535 0.0390 0.1135 35.0450

Mp10 0.1830 0.0360 0.2080 3.3530 0.9430 0.1590 0.2360 64.0400

97
Station: Palo Alto Statistical Summary

Date: 05/24/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 2.0793 0.2688 1.5136 33.5604 4.1308 0.8166 1.5784 417.3716

STD 1.0704 0.1667 0.8057 17.2467 2.3461 0.4445 0.8122 246.6757

SEM 0.378 0.059 0.285 6.098 0.829 0.157 0.287 87.213

CV% 51.480 62.041 53.228 51.390 56.794 54.434 51.456 59.102

n 88888888

r wt x [ ] 0.378 0.290 0.351 0.290 0.316 0.372 0.311 0.183

X 100mg 1.055 0.146 0.798 20.903 2.252 0.398 0.939 303.077

r l x [ ] 0.040 0.113 0.014 0.049 0.063 0.065 0.051 0.172

X 20mm 2.062 0.277 1.518 33.913 4.193 0.805 1.596 435.101

X 25mm 1.979 0.313 1.540 35.553 4.482 0.748 1.677 517.490

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.0960 0.0124 0.0704 1.5716 0.1924 0.0366 0.0752 19.5103

25mm 0.1683 0.0236 0.1277 2.9266 0.3598 0.0612 0.1421 40.2416

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.023 gm 0.053 gm

23.181 mg 53.482 mg

Estimated weight for 25mm clam

0.102 gm

102.291 mg

98
Station: Palo Alto Macoma petalum

Date: 05/24/06

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

Mp1 15.06 0.1506 0.0215 10 0.0427 0.0039 0.0274 0.6127 0.0655 0.0179 0.0275 7.552

Mp2 16.46 0.2958 0.0329 10 0.0573 0.006 0.0382 0.9929 0.1033 0.0193 0.0394 8.682

Mp3 17.55 0.7182 0.0399 10 0.0584 0.009 0.043 0.886 0.1209 0.0252 0.0467 10.76

Mp4 18.28 0.3183 0.0455 10 0.057 0.0085 0.0505 0.9832 0.1465 0.0284 0.0548 12.59

Mp5 19.53 0.4818 0.0482 15 0.0679 0.011 0.0515 0.9978 0.1422 0.0202 0.0502 12.79

Mp6 20.33 0.2404 0.0401 10 0.1 0.0152 0.0765 1.631 0.2211 0.0395 0.079 22.13

Mp7 21.55 0.8523 0.0775 10 0.0759 0.0081 0.0553 1.213 0.147 0.0251 0.0637 13.5

Mp8 22.64 0.3185 0.0796 10 0.0667 0.0072 0.0439 1.206 0.1137 0.0281 0.0478 16.61

MDL 0.0010 0.0004 0.0026 0.0011 0.0010 0.0033 0.0012 0.0037

MRL 0.0020 0.0008 0.0052 0.0021 0.0019 0.0066 0.0024 0.0073

Sample #

 Concentration (ug/g) ==> Mp1 2.8353 0.2590 1.8194 40.6839 4.3493 1.1886 1.8260 501.461

Mp2 1.9371 0.2028 1.2914 33.5666 3.4922 0.6525 1.3320 293.509

Mp3 0.8131 0.1253 0.5987 12.3364 1.6834 0.3509 0.6502 149.819

Mp4 1.7908 0.2670 1.5866 30.8891 4.6026 0.8922 1.7216 395.539

Mp5 2.1139 0.3425 1.6034 31.0648 4.4271 0.6289 1.5629 398.194

Mp6 4.1597 0.6323 3.1822 67.8453 9.1972 1.6431 3.2862 920.549

Mp7 0.8905 0.0950 0.6488 14.2321 1.7247 0.2945 0.7474 158.395

Mp8 2.0942 0.2261 1.3783 37.8650 3.5699 0.8823 1.5008 521.507

Sample #

 Content (ug) ==> Mp1 0.0610 0.0056 0.0391 0.8753 0.0936 0.0256 0.0393 10.7886

Mp2 0.0637 0.0067 0.0424 1.1032 0.1148 0.0214 0.0438 9.6467

Mp3 0.0324 0.0050 0.0239 0.4922 0.0672 0.0140 0.0259 5.9778

Mp4 0.0814 0.0121 0.0721 1.4046 0.2093 0.0406 0.0783 17.9857

Mp5 0.1019 0.0165 0.0773 1.4967 0.2133 0.0303 0.0753 19.1850

Mp6 0.1667 0.0253 0.1275 2.7183 0.3685 0.0658 0.1317 36.8833

Mp7 0.0690 0.0074 0.0503 1.1027 0.1336 0.0228 0.0579 12.2727

Mp8 0.1668 0.0180 0.1098 3.0150 0.2843 0.0703 0.1195 41.5250

99
Station: Palo Alto Statistical Summary

Date: 06/27/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 3.7417 0.4075 2.3141 54.3175 5.8938 1.2811 2.4248 441.9661

STD 0.8698 0.0954 0.6187 10.3505 1.3975 0.3945 0.6150 109.3769

SEM 0.290 0.032 0.206 3.450 0.466 0.131 0.205 36.459

CV% 23.247 23.403 26.735 19.056 23.712 30.791 25.361 24.748

n 99999999

r wt x [ ] 0.589 0.389 0.507 0.066 0.148 0.630 0.321 0.039

X 100mg 4.155 0.378 2.061 53.765 6.060 1.081 2.266 438.502

r l x [ ] 0.642 0.269 0.458 0.101 0.220 0.579 0.251 0.148

X 20mm 3.711 0.409 2.330 54.260 5.877 1.294 2.433 441.083

X 25mm 4.326 0.381 2.017 55.417 6.216 1.042 2.263 458.924

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.1666 0.0180 0.1013 2.4281 0.2613 0.0554 0.1068 19.5939

25mm 0.4023 0.0356 0.1865 5.2378 0.5728 0.0957 0.2092 43.0350

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.017 gm 0.045 gm

17.367 mg 45.305 mg

Estimated weight for 25mm clam

0.095 gm

95.313 mg

100
Station: Palo Alto Macoma petalum

Date: 06/27/06

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

Mp1 14.41 0.3111 0.0173 10 0.1084 0.0141 0.0941 1.679 0.1946 0.0554 0.0917 12.61

Mp2 16.51 0.7566 0.0270 15 0.1467 0.0189 0.1074 2.374 0.2518 0.0654 0.114 18.38

Mp3 17.48 0.8930 0.0271 15 0.2136 0.0245 0.1432 3.191 0.3433 0.0795 0.1413 24.98

Mp4 18.48 1.1779 0.0357 15 0.228 0.0268 0.1566 3.44 0.3609 0.0791 0.1533 28.56

Mp5 19.44 0.3576 0.0255 15 0.1184 0.0152 0.0851 1.864 0.2069 0.0478 0.0897 16.54

Mp6 20.42 0.6244 0.0568 10 0.1765 0.0219 0.1212 2.811 0.2924 0.0604 0.1236 25.26

Mp7 22.14 0.6661 0.0555 15 0.1639 0.0183 0.0997 2.666 0.2732 0.0593 0.1103 22.83

Mp8 23.57 0.3769 0.0942 10 0.1554 0.0122 0.059 1.971 0.1735 0.0354 0.0647 12.76

Mp9 29.77 0.1819 0.1819 10 0.0943 0.0066 0.0355 0.9982 0.1331 0.0157 0.0427 8.616

MDL 0.0010 0.0004 0.0026 0.0011 0.0010 0.0033 0.0012 0.0037

MRL 0.0020 0.0008 0.0052 0.0021 0.0019 0.0066 0.0024 0.0073

Sample #

 Concentration (ug/g) ==> Mp1 3.4844 0.4532 3.0248 53.9698 6.2552 1.7808 2.9476 405.336

Mp2 2.9084 0.3747 2.1293 47.0658 4.9921 1.2966 2.2601 364.393

Mp3 3.5879 0.4115 2.4054 53.6002 5.7665 1.3354 2.3735 419.597

Mp4 2.9035 0.3413 1.9942 43.8068 4.5959 1.0073 1.9522 363.698

Mp5 4.9664 0.6376 3.5696 78.1879 8.6787 2.0050 3.7626 693.792

Mp6 2.8267 0.3507 1.9411 45.0192 4.6829 0.9673 1.9795 404.548

Mp7 3.6909 0.4121 2.2452 60.0360 6.1522 1.3354 2.4839 514.112

Mp8 4.1231 0.3237 1.5654 52.2950 4.6033 0.9392 1.7166 338.551

Mp9 5.1842 0.3628 1.9516 54.8763 7.3172 0.8631 2.3474 473.667

Sample #

 Content (ug) ==> Mp1 0.0602 0.0078 0.0523 0.9328 0.1081 0.0308 0.0509 7.0056

Mp2 0.0786 0.0101 0.0575 1.2718 0.1349 0.0350 0.0611 9.8464

Mp3 0.0971 0.0111 0.0651 1.4505 0.1560 0.0361 0.0642 11.3545

Mp4 0.1036 0.0122 0.0712 1.5636 0.1640 0.0360 0.0697 12.9818

Mp5 0.1269 0.0163 0.0912 1.9971 0.2217 0.0512 0.0961 17.7214

Mp6 0.1605 0.0199 0.1102 2.5555 0.2658 0.0549 0.1124 22.9636

Mp7 0.2049 0.0229 0.1246 3.3325 0.3415 0.0741 0.1379 28.5375

Mp8 0.3885 0.0305 0.1475 4.9275 0.4338 0.0885 0.1618 31.9000

Mp9 0.9430 0.0660 0.3550 9.9820 1.3310 0.1570 0.4270 86.1600

101
102

10

Station: Palo Alto Statistical Summary

Date: 09/7/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 4.5854 0.4011 2.2707 65.8289 6.2469 1.4554 2.4549 383.1770

STD 0.8410 0.0429 0.3999 8.7555 0.4864 0.2027 0.3870 90.3851

SEM 0.266 0.014 0.126 2.769 0.154 0.064 0.122 28.582

CV% 18.341 10.684 17.610 13.300 7.786 13.927 15.763 23.588

n 10 10 10 10 10 10 10

r wt x [ ] 0.233 0.410 0.591 0.608 0.445 0.531 0.220 0.141

X 100mg 4.987 0.365 1.785 54.897 6.691 1.234 2.280 409.417

r l x [ ] 0.188 0.342 0.530 0.721 0.484 0.551 0.164 0.234

X 20mm 4.565 0.403 2.298 66.655 6.216 1.470 2.463 380.409

X 25mm 4.767 0.384 2.027 58.576 6.517 1.327 2.382 407.484

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.1712 0.0152 0.0854 2.4914 0.2362 0.0549 0.0923 14.1686

25mm 0.3486 0.0285 0.1502 4.3664 0.4855 0.0982 0.1764 29.4213

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.016 gm 0.038 gm

15.885 mg 37.984 mg

Estimated weight for 25mm clam

0.075 gm

74.693 mg
Station: Palo Alto Macoma petalum

Date: 09/7/06

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

Mp1 14.65 0.3433 0.0172 10 0.1766 0.0144 0.0834 2.8 0.2086 0.0563 0.084 11.83

Mp2 16.52 0.4439 0.0202 10 0.2283 0.0189 0.1053 3.274 0.2734 0.0681 0.1106 13.01

Mp3 17.52 0.5716 0.0229 10 0.1886 0.0216 0.1284 4.074 0.3142 0.0851 0.1274 22.38

Mp4 18.42 0.7265 0.0303 15 0.1819 0.0176 0.1041 3.103 0.2679 0.0669 0.1032 15.36

Mp5 19.44 0.4044 0.0337 10 0.1815 0.018 0.1197 2.53 0.2642 0.0651 0.1289 15.91

Mp6 20.54 0.2295 0.0383 10 0.0871 0.0097 0.0607 1.467 0.1622 0.0379 0.0614 9.698

Mp7 22.35 0.4266 0.0533 10 0.2346 0.0184 0.106 2.853 0.2592 0.0646 0.1239 23.22

Mp8 24.07 0.2619 0.0655 10 0.1506 0.0103 0.0428 1.353 0.1715 0.0252 0.0492 9.622

Mp9 25.24 0.1633 0.0817 10 0.0647 0.007 0.0287 0.8917 0.1042 0.0234 0.0358 8.239

Mp10 26.36 0.1844 0.0922 10 0.0925 0.0056 0.0374 1.254 0.1217 0.0247 0.0445 4.669

MDL 0.0015 0.0002 0.0026 0.0012 0.0008 0.0027 0.0266 0.0012

MRL 0.0029 0.0003 0.0090 0.0023 0.0011 0.0072 0.0532 0.0024

Sample #

 Concentration (ug/g) ==> Mp1 5.1442 0.4195 2.4294 81.5613 6.0763 1.6400 2.4468 344.597

Mp2 5.1431 0.4258 2.3722 73.7554 6.1590 1.5341 2.4916 293.084

Mp3 3.2995 0.3779 2.2463 71.2736 5.4969 1.4888 2.2288 391.533

Mp4 3.7557 0.3634 2.1493 64.0674 5.5313 1.3813 2.1308 317.137

Mp5 4.4881 0.4451 2.9599 62.5618 6.5331 1.6098 3.1874 393.422

Mp6 3.7952 0.4227 2.6449 63.9216 7.0675 1.6514 2.6754 422.571

Mp7 5.4993 0.4313 2.4848 66.8776 6.0759 1.5143 2.9044 544.304

Mp8 5.7503 0.3933 1.6342 51.6609 6.5483 0.9622 1.8786 367.392

Mp9 3.9620 0.4287 1.7575 54.6050 6.3809 1.4329 2.1923 504.532

Mp10 5.0163 0.3037 2.0282 68.0043 6.5998 1.3395 2.4132 253.200

Sample #

 Content (ug) ==> Mp1 0.0883 0.0072 0.0417 1.4000 0.1043 0.0282 0.0420 5.9150

Mp2 0.1038 0.0086 0.0479 1.4882 0.1243 0.0310 0.0503 5.9136

Mp3 0.0754 0.0086 0.0514 1.6296 0.1257 0.0340 0.0510 8.9520

Mp4 0.1137 0.0110 0.0651 1.9394 0.1674 0.0418 0.0645 9.6000

Mp5 0.1513 0.0150 0.0998 2.1083 0.2202 0.0543 0.1074 13.2583

Mp6 0.1452 0.0162 0.1012 2.4450 0.2703 0.0632 0.1023 16.1633

Mp7 0.2933 0.0230 0.1325 3.5663 0.3240 0.0808 0.1549 29.0250

Mp8 0.3765 0.0258 0.1070 3.3825 0.4288 0.0630 0.1230 24.0550

Mp9 0.3235 0.0350 0.1435 4.4585 0.5210 0.1170 0.1790 41.1950

Mp10 0.4625 0.0280 0.1870 6.2700 0.6085 0.1235 0.2225 23.3450

103
Station: Palo Alto Statistical Summary

Date: 10/19/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 7.8588 0.4774 3.5447 82.7916 7.5848 1.9702 3.9238 425.3945

STD 2.8262 0.0819 1.1570 15.9100 1.8535 0.5410 1.0835 96.6388

SEM 0.942 0.027 0.386 5.303 0.618 0.180 0.361 32.213

CV% 35.963 17.150 32.641 19.217 24.437 27.456 27.614 22.717

n 99999999

r wt x [ ] 0.502 0.590 0.254 0.566 0.291 0.115 0.178 0.738

X 100mg 11.012 0.370 2.892 102.807 8.784 1.832 4.353 266.852

r l x [ ] 0.459 0.542 0.209 0.395 0.333 0.133 0.229 0.621

X 20mm 7.878 0.477 3.541 82.883 7.594 1.969 3.927 424.521

X 25mm 9.695 0.415 3.202 91.697 8.459 1.868 4.275 340.458

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.2981 0.0184 0.1323 3.2270 0.2927 0.0746 0.1500 16.0711

25mm 0.7002 0.0340 0.2461 7.1933 0.6486 0.1446 0.3261 27.3144

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.015 gm 0.039 gm

15.446 mg 39.363 mg

Estimated weight for 25mm clam

0.081 gm

81.327 mg

104
Station: Palo Alto Macoma petalum

Date: 10/19/06

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

Mp1 14.61 0.1139 0.0127 10 0.1105 0.0073 0.0525 1.106 0.1072 0.0315 0.0502 6.293

Mp2 16.51 0.2439 0.0244 10 0.1562 0.012 0.0832 1.675 0.1485 0.0419 0.0845 10.55

Mp3 17.80 0.3341 0.0304 10 0.184 0.0134 0.0964 2.281 0.1927 0.0527 0.0932 13.12

Mp4 18.50 0.3022 0.0302 10 0.1858 0.0128 0.0893 2.16 0.199 0.0544 0.1031 11.4

Mp5 19.48 0.3470 0.0347 10 0.257 0.0166 0.1282 2.803 0.242 0.0684 0.1438 17.36

Mp6 20.96 0.1953 0.0391 10 0.1195 0.011 0.1161 1.563 0.1692 0.0526 0.1137 9.297

Mp7 22.36 0.1539 0.0513 10 0.1381 0.0075 0.0288 1.053 0.124 0.0176 0.0403 7.861

Mp8 23.35 0.2334 0.0778 10 0.1424 0.0096 0.073 2.584 0.1319 0.0392 0.0794 7.977

Mp9 25.96 0.0902 0.0902 10 0.1296 0.0036 0.0307 0.8989 0.0998 0.0215 0.0474 2.207

MDL 0.0015 0.0002 0.0026 0.0012 0.0008 0.0027 0.0266 0.0012

MRL 0.0029 0.0003 0.0090 0.0023 0.0011 0.0072 0.0532 0.0024

Sample #

 Concentration (ug/g) ==> Mp1 9.7015 0.6409 4.6093 97.1027 9.4118 2.7656 4.4074 552.502

Mp2 6.4043 0.4920 3.4112 68.6757 6.0886 1.7179 3.4645 432.554

Mp3 5.5073 0.4011 2.8854 68.2730 5.7677 1.5774 2.7896 392.697

Mp4 6.1482 0.4236 2.9550 71.4758 6.5850 1.8001 3.4116 377.234

Mp5 7.4063 0.4784 3.6945 80.7781 6.9741 1.9712 4.1441 500.288

Mp6 6.1188 0.5632 5.9447 80.0307 8.6636 2.6933 5.8218 476.037

Mp7 8.9734 0.4873 1.8713 68.4211 8.0572 1.1436 2.6186 510.786

Mp8 6.1011 0.4113 3.1277 110.7112 5.6512 1.6795 3.4019 341.774

Mp9 14.3681 0.3991 3.4035 99.6563 11.0643 2.3836 5.2550 244.678

Sample #

 Content (ug) ==> Mp1 0.1228 0.0081 0.0583 1.2289 0.1191 0.0350 0.0558 6.9922

Mp2 0.1562 0.0120 0.0832 1.6750 0.1485 0.0419 0.0845 10.5500

Mp3 0.1673 0.0122 0.0876 2.0736 0.1752 0.0479 0.0847 11.9273

Mp4 0.1858 0.0128 0.0893 2.1600 0.1990 0.0544 0.1031 11.4000

Mp5 0.2570 0.0166 0.1282 2.8030 0.2420 0.0684 0.1438 17.3600

Mp6 0.2390 0.0220 0.2322 3.1260 0.3384 0.1052 0.2274 18.5940

Mp7 0.4603 0.0250 0.0960 3.5100 0.4133 0.0587 0.1343 26.2033

Mp8 0.4747 0.0320 0.2433 8.6133 0.4397 0.1307 0.2647 26.5900

Mp9 1.2960 0.0360 0.3070 8.9890 0.9980 0.2150 0.4740 22.0700

105
106

12

Station: Palo Alto Statistical Summary

Date: 12/18/06

Ag Cd Cr Cu Ni Pb V Zn

Mean(ug/g) 7.6356 0.5702 4.6043 67.0780 7.8999 2.4053 5.4801 445.9620

STD 1.4641 0.0687 0.5151 10.5804 0.7377 0.2338 1.1216 66.7346

SEM 0.423 0.020 0.149 3.054 0.213 0.067 0.324 19.265

CV% 19.175 12.052 11.187 15.773 9.338 9.719 20.468 14.964

n 12 12 12 12 12 12 12

r wt x [ ] 0.485 0.843 0.142 0.613 0.534 0.441 0.288 0.876

X 100mg 5.681 0.411 4.805 49.240 6.817 2.121 6.369 285.168

r l x [ ] 0.594 0.888 0.076 0.689 0.695 0.573 0.038 0.892

X 20mm 7.258 0.544 4.587 63.910 7.677 2.347 5.499 420.118

X 25mm 5.693 0.434 4.517 50.787 6.754 2.106 5.576 313.055

Estimated content (ug) for 15mm and 20mm clam

Ag Cd Cr Cu Ni Pb V Zn

20mm 0.2874 0.0219 0.1854 2.5636 0.3107 0.0950 0.2178 16.7812

25mm 0.5196 0.0404 0.3965 4.7373 0.6137 0.1903 0.4694 29.5528

Estimated weight for 15mm clam Estimated weight for 20mm clam

0.015 gm 0.041 gm

14.864 mg 40.832 mg

Estimated weight for 25mm clam

0.089 gm

89.417 mg
Station: Palo Alto Macoma petalum

Date: 12/18/06

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

Mp1 14.31 0.1581 0.0144 10 0.1394 0.0098 0.0782 1.372 0.1414 0.0421 0.1017 7.624

Mp2 16.50 0.1767 0.0196 10 0.1498 0.0112 0.0817 1.229 0.1567 0.0446 0.1131 9.207

Mp3 16.51 0.2077 0.0208 10 0.1801 0.0133 0.1056 1.567 0.1719 0.0539 0.13 10.45

Mp4 17.51 0.2944 0.0268 10 0.2274 0.0187 0.1345 1.587 0.2348 0.0719 0.1676 14.57

Mp5 17.56 0.2751 0.0250 10 0.2321 0.0174 0.1383 1.912 0.2407 0.074 0.1597 13.73

Mp6 18.43 0.2527 0.0316 10 0.2068 0.0146 0.1092 1.719 0.1859 0.0574 0.1221 11.32

Mp7 18.48 0.1901 0.0272 10 0.1853 0.0117 0.0778 1.461 0.1573 0.0486 0.0626 8.718

Mp8 19.55 0.2718 0.0388 10 0.1728 0.0143 0.1433 1.674 0.2122 0.0679 0.1323 11.41

Mp9 19.41 0.2721 0.0340 10 0.2117 0.014 0.0976 2.055 0.1863 0.0516 0.1033 13.04

Mp10 20.40 0.2988 0.0427 10 0.133 0.0149 0.1306 1.607 0.2051 0.0643 0.1716 11.74

Mp11 21.94 0.3236 0.0539 10 0.1927 0.0163 0.1352 1.914 0.2401 0.075 0.1771 10.84

Mp12 24.92 0.3035 0.1012 10 0.2132 0.0135 0.1572 1.664 0.2251 0.0685 0.2175 9.641

MDL 0.0015 0.0002 0.0026 0.0012 0.0008 0.0027 0.0266 0.0012

MRL 0.0029 0.0003 0.0090 0.0023 0.0011 0.0072 0.0532 0.0024

Sample #

 Concentration (ug/g) ==> Mp1 8.8172 0.6199 4.9462 86.7805 8.9437 2.6629 6.4326 482.226

Mp2 8.4776 0.6338 4.6237 69.5529 8.8681 2.5241 6.4007 521.053

Mp3 8.6712 0.6403 5.0843 75.4454 8.2764 2.5951 6.2590 503.130

Mp4 7.7242 0.6352 4.5686 53.9063 7.9755 2.4423 5.6929 494.905

Mp5 8.4369 0.6325 5.0273 69.5020 8.7495 2.6899 5.8052 499.091

Mp6 8.1836 0.5778 4.3213 68.0253 7.3565 2.2715 4.8318 447.962

Mp7 9.7475 0.6155 4.0926 76.8543 8.2746 2.5565 3.2930 458.601

Mp8 6.3576 0.5261 5.2723 61.5894 7.8072 2.4982 4.8675 419.794

Mp9 7.7802 0.5145 3.5869 75.5237 6.8467 1.8964 3.7964 479.236

Mp10 4.4511 0.4987 4.3708 53.7818 6.8641 2.1519 5.7430 392.905

Mp11 5.9549 0.5037 4.1780 59.1471 7.4197 2.3177 5.4728 334.981

Mp12 7.0247 0.4448 5.1796 54.8270 7.4168 2.2570 7.1664 317.661

Sample #

 Content (ug) ==> Mp1 0.1267 0.0089 0.0711 1.2473 0.1285 0.0383 0.0925 6.9309

Mp2 0.1664 0.0124 0.0908 1.3656 0.1741 0.0496 0.1257 10.2300

Mp3 0.1801 0.0133 0.1056 1.5670 0.1719 0.0539 0.1300 10.4500

Mp4 0.2067 0.0170 0.1223 1.4427 0.2135 0.0654 0.1524 13.2455

Mp5 0.2110 0.0158 0.1257 1.7382 0.2188 0.0673 0.1452 12.4818

Mp6 0.2585 0.0183 0.1365 2.1488 0.2324 0.0718 0.1526 14.1500

Mp7 0.2647 0.0167 0.1111 2.0871 0.2247 0.0694 0.0894 12.4543

Mp8 0.2469 0.0204 0.2047 2.3914 0.3031 0.0970 0.1890 16.3000

Mp9 0.2646 0.0175 0.1220 2.5688 0.2329 0.0645 0.1291 16.3000

Mp10 0.1900 0.0213 0.1866 2.2957 0.2930 0.0919 0.2451 16.7714

Mp11 0.3212 0.0272 0.2253 3.1900 0.4002 0.1250 0.2952 18.0667

Mp12 0.7107 0.0450 0.5240 5.5467 0.7503 0.2283 0.7250 32.1367

107
108

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). 

Note: Appendix tables in this document may not be 508 complaint. 508 compliant Excel spreadsheet 

containing these tables may be access at URL: http://pubs.usgs.gov/of/2007/1199/Appendix-D.xls 
D-1a. Mercury and selenium concentrations (μg/g dry weight) determined in surface sediments and 

M. petalum in 2006. One analysis was conducted on homogenized sediment. Values for M. petalum

are the mean and 95% confidence interval (n=3). Not analyzed (NA). 

Date

mercury selenium mercury selenium

1/9/2006 0.21 0.84 NA NA

2/7/2006 0.22 0.62 0.31±0.02 6.47±0.14

4/24/2006 0.25 0.57 0.16±0.02 4.80±0.04

6/27/2006 0.2 0.4 0.27±0.02 4.17±0.03

9/7/2006 0.24 0.42 0.37±0.03 4.47±0.03

12/18/2006 0.3 0.4 0.49±0.02 6.27±0.03

Sediment M. petalum

D-1b. Mercury and selenium concentrations (μg/g dry weight) determined in sample splits of surface 

sediments and M. petalum collected in April and June 2006. 

Date

mercury selenium mercury selenium

4/24/2006 NA NA 0.22/0.22 NA

6/27/2006 0.19/0.21 0.4/0.4 NA 4.1/4.2

Sediment M. petalum

109
D-2. Observed and certified concentrations of mercury and selenium in standard reference materials 

analyzed in 2006. Certified concentrations as reported by National Research Council Canada are the 

mean and 95% confidence interval. The five materials are oyster tissue (NIST 1566b), lobster 

hepatopancreas (TORT-2), dogfish muscle (DORM-2), San Joaquin soil (NIST 2709), and marine 

sediment (USGS MAG-1). Split values indicate standard was used more than once during the year 

for sample analysis 

SRM

Observed Certified Observed Certified

NIST 1566B 0.03/0.05 0.04±0.01 2.2/1.9 2.06±0.15

TORT-2 0.3 0.27±0.06 6.3 5.6±0.7

DORM-2 4.4 4.64±0.26 1.5 1.4±0.1

NIST 2709 1.3 1.4±0.1 1.6 1.5±0.1

USGS MAG-1 0.03 0.02 1.3 1.2±0.1

Mercury Selenium

110
111

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. 

Note: Appendix tables in this document may not be 508 complaint. 508 compliant Excel spreadsheet 

containing these 5 08 compliant tables may be accessed at URL: 

http://pubs.usgs.gov/of/2007/1199/Appendix-E.xls 
E1. Observed and certified concentrations in SRM 2709. Units in upper table are μg/mL. The lower table reports the percent recovery.

Month Rep AG AL AS CD CR CU FE MN NI PB V ZN

January 1 1.097115 43823.65 15.52215 1.970744 101.4019 34.43722 35432.8 542.87 88.1349 39.43519 95.55059 107.6392

2 1.183915 43988.57 13.67626 2.122882 96.97898 34.23148 31741.2 496.43 78.1384 26.18902 88.65075 96.61155

February 1 0.983343 43668.47 13.16476 2.127233 99.39795 34.59763 32450.3 498.09 80.91511 26.47 95.36424 101.8663

2 0.971644 44457.66 14.11858 2.300218 99.74222 36.12929 33670.4 524.69 84.87012 27.26552 95.43922 107.7732

March 1 1.147306 44376.15 13.39889 2.110223 97.00881 34.2143 32001.6 499.49 78.56997 26.55194 88.54743 98.03319

2 1.097645 44729.02 13.26321 2.195289 98.12486 34.94169 32997.9 514.75 80.58541 26.45781 92.31649 100.6174

April 1 1.03912 43663.41 12.87694 2.03749 98.55338 34.51508 32722.1 500.61 80.70497 26.22249 94.2339 101.4874

2 0.859207 42804.14 13.66921 2.479984 96.85608 34.99317 33372.4 522.94 85.78403 28.13904 87.13142 102.9291

May 1 0.915157 42306.96 14.90944 2.669209 95.99619 34.85224 34070.5 530.79 88.54147 29.09438 87.87417 104.4042

2 0.883179 43837.82 13.04697 2.067443 98.21357 34.40385 32356.5 502.21 80.28904 26.71618 91.77037 100.3011

June 1 1.010101 46187.36 15.58724 2.040008 104.3177 36.52208 36878.6 565.66 91.06754 40.22579 98.3363 113.3096

2 1.053887 45675.08 16.84231 3.221316 107.5363 38.19845 37462.7 582.22 96.59972 31.27858 101.2527 105.6671

September 1 0.909971 41548.89 15.12101 2.14908 96.18587 34.77251 35547 561.67 88.49952 38.8577 90.08712 109.0416

2 1.27501 42546.1 14.79011 1.824245 97.76383 34.89604 34778.3 535.7 85.17066 37.21067 91.58494 105.8847

October 1 1.28808 47066.04 17.82866 2.412595 111.1634 38.00859 40012.3 615.82 101.8197 45.77796 103.7007 122.5516

2 0.986114 43650.63 14.81183 1.77098 99.47676 34.87623 34393.2 533.71 82.59207 35.9831 97.26303 119.2795

December 1 1.151981 46645.11 16.6734 2.12207 108.9733 37.14632 38156.8 584.88 94.96766 42.34034 101.0711 120.6548

1.715593 43290.13 16.4125 2.230271 103.1453 36.59931 37590.5 577.2 95.84445 42.77545 101.3534 118.2234

Cert. Value 0.41 75000 17.70 0.38 130.00 34.60 35000 538 88.0 18.9 112.0 106.0

Std 0.03 0.06 0.80 0.01 4.00 0.70 0.11 17.00 5.00 0.50 5.00 3.00

Month Rep AG AL AS CD CR CU FE MN NI PB V ZN

January 1 267.6 58.43 87.70 518.6 78.00 99.53 101.24 100.90 100.15 208.65 85.31 101.55

2 288.8 58.65 77.27 558.7 74.60 98.93 90.69 92.27 88.79 138.57 79.15 91.14

February 1 239.8 58.22 74.38 559.8 76.46 99.99 92.72 92.58 91.95 140.05 85.15 96.10

2 237.0 59.28 79.77 605.3 76.72 104.42 96.20 97.53 96.44 144.26 85.21 101.67

March 1 279.8 59.17 75.70 555.3 74.62 98.89 91.43 92.84 89.28 140.49 79.06 92.48

2 267.7 59.64 74.93 577.7 75.48 100.99 94.28 95.68 91.57 139.99 82.43 94.92

April 1 253.4 58.22 72.75 536.2 75.81 99.75 93.49 93.05 91.71 138.74 84.14 95.74

2 209.6 57.07 77.23 652.6 74.50 101.14 95.35 97.20 97.48 148.88 77.80 97.10

May 1 223.2 56.41 84.2 702.4 73.8 100.7 97.34 98.66 100.6 153.9 78.5 98.5

2 215.4 58.45 73.7 544.1 75.5 99.4 92.45 93.35 91.2 141.4 81.9 94.6

June 1 246.4 61.58 88.06 536.8 80.24 105.56 105.37 105.14 103.49 212.83 87.80 106.90

2 257.0 60.90 95.15 847.7 82.72 110.40 107.04 108.22 109.77 165.50 90.40 99.69

September 1 221.9 55.40 85.43 565.5 73.99 100.50 101.56 104.40 100.57 205.60 80.43 102.87

2 311.0 56.73 83.56 480.1 75.20 100.86 99.37 99.57 96.78 196.88 81.77 99.89

October 1 314.2 62.75 100.73 634.9 85.51 109.85 114.32 114.47 115.70 242.21 92.59 115.61

2 240.5 58.20 83.68 466.0 76.52 100.80 98.27 99.20 93.85 190.39 86.84 112.53

December 1 281.0 62.19 94.20 558.4 83.83 107.36 109.02 108.71 107.92 224.02 90.24 113.83

AVG 256.1 58.90 82.85 582.4 77.27 102.30 98.83 99.63 98.08 172.49 84.04 100.89

STDEV 31.6 2.03 8.31 90.0 3.61 3.77 6.79 6.57 7.68 35.88 4.49 7.39

112
113

E-2. Observed and certified values for inorganic elements in NIST Standard Reference Material 

2976 (mussel tissue) and DOLT-3 (dogfish liver) prepared in 2006. Values for different dates are 

the observed mean concentrations and 1 standard deviation for either replicate or triplicates of the 

standard (n=2-3). The mean values are summarized as the median. The certified values for the 

standard reference material are shown below the observed values (vanadium is not certified for this 

material). All values are reported as μg/g dry weight. Two different SRMs were used this year due 

insufficient amount of material during time of processing. 

NIST 2976

Date Cadmium Chromium Copper Lead Nickel Silver Vanadium Zinc

January 9, 2006 0.65 0.72 4.48 1.05 0.63 0.03 0.76 138.01

February 7, 2006 0.66 0.48 4.29 0.94 0.63 0.02 0.71 135.74

Mean 0.65 0.60 4.38 1.00 0.63 0.03 0.74 136.88

STD 0.01 0.17 0.14 0.08 0.00 0.01 0.03 1.61

Certified Values

Mean 0.82 0.5 4.02 1.19 0.93 0.011 not certified 137

Max. 0.98 0.66 4.35 1.37 1.05 0.016 150

Min. 0.66 0.37 3.69 1.01 0.81 0.006 124

DOLT-3

Date Cadmium Chromium Copper Lead Nickel Silver Vanadium Zinc

March 22, 2006 19.83 4.27 34.63 0.13 3.04 1.34 0.32 94.32

April 24, 2006 19.41 4.05 33.17 0.20 2.86 1.16 0.32 92.70

May 31, 2006 19.36 3.68 33.33 0.22 2.35 1.12 0.33 93.11

June 27, 2006 19.89 4.39 35.75 0.23 3.03 1.39 0.36 94.87

September 7, 2006 19.29 5.40 35.30 0.26 3.90 1.38 0.34 92.89

October 19, 2006 19.15 4.40 35.35 0.27 3.27 1.37 0.34 92.31

December 18, 2006 19.12 4.27 36.31 0.24 3.31 1.41 0.76 93.88

Mean 19.44 4.35 34.83 0.22 3.11 1.31 0.40 93.44

STD 0.31 0.53 1.20 0.05 0.47 0.12 0.16 0.93

Certified Values

Mean 19.4 not certified 31.2 0.319 2.72 1.2 not certified 86.6

Max. 20 32.2 0.364 3.07 1.27 89

Min. 18.8 30.2 0.274 2.37 1.13 84.2
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. Note: Appendix tables in this document may not be 508 complaint. 508 compliant Excel spreadsheet containing these 

may be accessed at URL: http://pubs.usgs.gov/of/2007/1199/Appendix-F.xls 

114
115

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. 

b 

0.0160.007

0.003

0.008

P

0.00150.00110.0006

0.0008

Method marker Ag Al Cd Cr Cu Fe Mn Ni

Sediment MDL 0.0015 0.4500 0.0005 0.0031 0.0028 0.055 0.0058

MRL 0.0031 0.8900 0.001 0.0064 0.0055 0.108 0.0116

Tissue MDL 0.0015 0.1399 0.0002 0.0045 0.0012 0.0056 0.0003

MRL 0.0029 0.2798 0.0003 0.009 0.0023 0.0111 0.0006 
116

Appendix G 

Reproduction data for the year 2006 (G-1). 

Note: Appendix tables in this document may not be 508 complaint. 508 compliant Excel spreadsheet 

containing these 508 compliant tables may be accessed at URL: 

http://pubs.usgs.gov/of/2007/1199/Appendix-G.xls 
117

G-1. Reproductive stage of M. petalum sampled from Palo Alto during 2006. 

Date Inactive Active Ripe Spawning Spent Spawned N Reproductive Non-Reproductive

1/9/06 0 0 100 0 0 10 100 0

2/7/06 0 0 60 40 0 10 100 0

3/1/06 0 0 100 0 0 10 100 0

4/24/06 0 0 50 40 10 10 90 -10

5/31/06 0 0 0 0 100 10 0 -100

6/27/06 80 0 0 0 20 10 0 -100

9/7/06 60 10 0 0 30 10 10 -90

12/18/06 0 33.3 66.7 0 0 9 100 0
Appendix H 

Complete list of benthic species found at Palo Alto in the year 2006. Note: Appendix tables in this document may not be 508 complaint. 508 compliant Excel spreadsheet containing these accessed at URL: http://pubs.usgs.gov/of/2007/1199/Appendix-H.xls 

118
Species Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev 

Acari 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Actiniaria 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Ampelisca abdita 1.3 0.6 3.0 1.7 1.7 1.2 0.7 0.6 0.0 0.0 1.0 1.0 2.3 1.5 12.7 0.6 0.7 1.Ampithoe spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Anthozoa 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Balanus ?aquila 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Balanus improvisus 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Balanus spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 11.7 13.2 0.3 0.6 1.7 2.1 0.0 0.Boonea bisuturalis 0.0 0.0 0.3 0.6 0.3 0.6 0.3 0.6 0.3 0.6 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.Calinoida 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Callianassidae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Capitella "capitata" 0.0 0.0 0.0 0.0 0.7 0.6 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.Caprella californica 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Cirratulidae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Cirripedia 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Corbula amurensis 0.3 0.6 0.0 0.0 24.7 3.1 7.7 2.1 4.3 1.2 3.3 1.2 4.3 2.1 2.7 1.5 8.0 1.Corophium ?insidiosum 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.

Corophium alienense 1.3 1.2 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 2.0 2.6 3.3 2.9 2.3 1.2 2.7 2.Corophium spinicorne 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Cumella vulgaris 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Cyprideis spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Dynamenella spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Eogammarus confervicolus 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Eteone ?californica 2.3 4.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Eteone lighti 5.3 5.5 2.3 1.5 5.7 0.6 4.3 4.0 1.3 0.6 0.3 0.6 2.0 1.7 1.7 2.9 7.7 3.Eteone spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.7 1.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Euchone limnicola 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Euchone spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Eusarsiella zostericola 5.3 4.9 5.0 2.0 5.0 3.6 2.7 3.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Gemma gemma 232.3 205.5 230.0 22.5 364.3 55.8 334.3 36.5 22.0 9.6 23.0 4.6 32.0 10.0 32.7 13.6 132.7 53.Glycera spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Glycinde armigera 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Glycinde polygnatha 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Glycinde spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Gnorisphaeroma oregonensis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.7 1.2 1.3 1.5 0.7 0.6 0.3 0.6 0.0 0.Grandidierella japonica 5.3 1.5 1.3 0.6 6.0 5.0 0.3 0.6 9.7 6.4 21.7 10.3 17.0 11.5 1.7 0.6 6.7 1.

09-Jan-06 07-Feb-06 22-Mar-06 18-Apr-06 25-May-06 14-Jun-06 25-Jul-06 23-Aug-06 21-Sep-06 

119
Species Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev 

Harmothoe imbricata 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Harpacticoida 0.0 0.0 0.0 0.0 0.0 0.0 5.7 9.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Hemigrapsus oregonensis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Heteromastus filiformis 14.0 1.0 11.0 4.6 19.3 3.8 14.3 13.8 14.3 4.0 17.0 3.6 9.0 4.6 22.0 9.0 18.0 6.Ilyanassa obsoleta 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Macoma petalum 3.0 2.6 2.0 1.0 1.7 2.1 4.0 4.0 21.3 7.1 18.0 1.7 17.3 2.3 20.3 2.3 18.3 3.

Macoma spp. 0.0 0.0 0.0 0.0 3.0 1.0 6.7 2.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Marphysa sanguinea 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Melita nitida 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.Moncorophium acherusicum 0.3 0.6 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.0 1.7 2.9 0.0 0.0 37.0 20.Moncorophium insidiosum 1.7 1.5 0.0 0.0 0.3 0.6 0.0 0.0 0.7 1.2 0.0 0.0 0.0 0.0 0.7 1.2 0.0 0.Moncorophium spp. 0.7 1.2 1.3 0.6 1.7 2.1 0.0 0.0 0.7 0.6 0.0 0.0 0.3 0.6 0.0 0.0 3.7 3.Musculista senhousia 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Mya arenaria 0.0 0.0 0.0 0.0 1.0 0.0 2.3 1.2 0.0 0.0 1.0 1.0 0.3 0.6 0.0 0.0 0.0 0.Mysidacea 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Naididae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Neanthes succinea 0.3 0.6 0.3 0.6 0.7 0.6 0.3 0.6 0.0 0.0 0.0 0.0 1.0 0.0 0.3 0.6 0.0 0.Nematoda 23.0 13.1 0.0 0.0 1.7 2.1 1.3 2.3 18.0 26.0 16.3 23.2 7.7 12.4 12.0 13.1 14.7 6.Nippoleucon hinumensis 16.0 2.6 32.0 20.1 81.0 19.0 227.7 37.9 20.3 6.4 1.0 1.0 3.3 1.5 18.3 6.0 32.7 13.Odostomia fetella 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Odostomia spp. 1.7 2.1 0.7 0.6 1.0 0.0 2.3 2.1 0.3 0.6 0.3 0.6 0.0 0.0 0.0 0.0 1.3 1.Oligochaeta 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Planariidae A 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.7 1.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Polydora cornuta 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.7 0.6 0.0 0.Polydora spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.Pseudopolydora kempi 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.0 0.0 0.Rochefortia grippi 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Rochefortia spp. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Sabaco elongatus 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Sphaeromatidae (juv.) 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Sphaerosyllis californiensis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Sphaerosyllis erinaceus 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Streblospio benedicti 0.0 0.0 6.3 5.0 19.7 10.5 8.3 13.6 13.0 4.4 4.0 6.1 4.0 4.0 14.3 5.5 9.3 4.Synidotea laevidorsalis 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.7 0.6 0.0 0.0 0.0 0.0 4.3 3.Tellinidae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Tharyx spp. ? 0.3 0.6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Tubificidae 56.7 24.9 21.7 19.7 23.7 11.0 27.3 17.5 37.3 19.3 23.0 7.2 27.3 32.3 28.3 9.9 38.7 25.Turbellaria 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.

09-Jan-06 07-Feb-06 22-Mar-06 18-Apr-06 25-May-06 14-Jun-06 25-Jul-06 23-Aug-06 21-Sep-06 

120
121

Species Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev Mean St Dev 

Unid. Amphipod 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.

Unid. Balanomorpha 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Bivalvia 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Cumacea 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Gastropoda 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Isopoda 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Nudibranchia 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Ostracoda 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Polychaeta 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Spionidae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Syllidae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.Unid. Tanaidacea 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.3 0.6 0.0 0.Urosalpinx cinerea 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.

09-Jan-06 07-Feb-06 22-Mar-06 18-Apr-06 25-May-06 14-Jun-06 25-Jul-06 23-Aug-06 21-Sep-06