HomeMy WebLinkAboutStaff Report 197-07City of Palo ALto
Manager’s Report
TO:
FROM:CITY MANAGER DEPARTMENT: PUBLIC WORKS
DATE:APRIL 16, 2007 CMR:197:07
SUBJECT:APPROVAL OF A THREE-YEAR EXTENSION TO THE AGREEMENT
WITH THE UNITED STATES GEOLOGICAL SURVEY IN THE TOTAL
AMOUNT OF $186,000 FOR SAN FRANCISCO BAY MONITORING
RECOMMENDATION
Staff recommends that Council approve and authorize the City Manager or his designee to execute
the attached extension to Contract No. C05109138 with the United States Geologic Survey
(U.S.G.S.) in the amount of $186,000 to monitor pollutants in clam tissue and sediments and to
monitor ecosystem diversity in the Palo Alto Baylands area of San Francisco Bay during calendar
years 2007-2009.
DISCUSSION
Project Description
The work to be done by the U.S.G.S. consists of two parts. Pa~t, I provides for sampling and analysis
of tissue from clams and sediment found in the mud flats near the discharge point of the Regional
Water Quality Control Plant (RWQCP). Part II provides for monitoring ofthe number and diversity
of the benthic (bottom dwelling) organisms and the reproduetivity of the clams. The monitoring is
required by the San Francisco Bay Regional Water Quality Control Board (Regional Board), which
regulates the discharge of treated wastewater to the Bay by Palo Alto. The sampling will cover a
three-year period (calendar years 2007 - 2009), and continue the work approved by Council and
completed during the past three years (CMR:416:04).
The results to date show dramatic decreases in pollutant levels in the clams compared to the early
1980s when pollutant discharges from the RWQCP were much greater. Part II of the program has
shown that the clams are better able to reproduce and that certain other benthic Organisms are on the
increase, consistent with a less contaminated environment.
Selection Process
The U.S.G.S. has collected clam and sediment data adjacent to the Palo Alto discharge point since
1974. Much data on diversity and clam reproductivity has also been collected at that.location. No
other consultants or institutions have the unique capability to analyze pollutant and ecosystem trends
in the vicinity. The work done by the U.S.G.S. for Palo Alto to date has been exemplary and
received nationwide recognition. The U.S.G.S. does not charge Palo Alto for the full cost of the
sampling program, but only for incremental costs associated with Palo Alto’s required monitoring.
The Regional Board and the City wish to take advantage of the knowledge, experience, and
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CMR:197:07 Page 1 of 2
efficiency in analyzing and interpreting data that the U.S.G.S. is able to bring to this project. For
these reasons, the U.S.G.S. has been declared a sole source provider of the required services.
RESOURCE IMPACT
The total cost of the three-year extension agreement is $186,000. First year costs in the amount of
$62,000 will be funded from the fiscal year 2006-07 Wastewater Treatment Fund operating budget.
It is anticipated that funds for the second year ($62,000) and the third year ($62,000) will be included
in subsequent budgets. The agreement acknowledges that it is "subject to the availability of
appropriations."
POLICY IMPLICATIONS
Approving this continuing monitoring program does not have any new policy implications.
ENVIRONMENTAL REVIEW
The monitoring program does not constitute a project under the California Environmental Quality
Act and, therefore, an environmental assessment is not required.
ATTACHMENT
Attachment A: Agreement with U.S.G.S.
PREPARED BY:
DEPARTMENT HEAD:
CITY MANAGER APPROVAL:
PHILIP L. BOBEL
GLENN S. ROBERTS
Director of Public Works
EMILY HARRISON
Assistant City Manager
CMR:197:07 Page 2 of 2
ATTACHMENT A
UNITED STATES DEPARTMENT OF THE ]iNTERIOR
U.S. GEOLOGICAL SURVEY
AMENDMENT OF JOINT FUNDING AGREEMENT
FOR
WATER RESOURCES INVESTIGATIONS
Customer #: CA221
Agreement 04H4CADIR000010
TIN #: 94-6000389
Fixed Cost Agreement: Yes
This is Amendment I for the USGS Joint Funding Agreement 04H4CAWR000010 (Reference Polo Alto
City Contract # C05109138) dated January 1, 2004.
1. The parties hereto agree that subject to. the availability of appropriations and in accordance with their
respective authorities there shall be maintained in cooperation Near Field Receiving Water Monitoring of (1)
Tissues and Sediments and (2) Benthic Community herein called the program.
2. Paragraph 2a of the agreement’s period of performance is hereby extended by 3 years to now read as
follows:
(a) $0 by the party of the first part (USGS) during the period January 1, 2004 to April 30, 2010
3. Paragraph 2b of the agreement’s funding amount is increased by $186,000 and the agreement’s period of
performance is hereby extended by 3 years to now read as follows:
(b)$372,000 by the party of the second part (City of Polo Alto) during the period January 1, 2004 to April
30, 2010
4. The Billing Terms and Conditions listed in Paragraph 2b of the agreement are now changed to read as
follows:
The City of Palo Alto will allocate funds for this project annually to the USGS in increments of the
following for Part (1), $41,000 in 2004, $41,000 in 2005, $41,000 in 2006, $41,000 in 2007, $41,000 in
2008, $41,000 in 2009; and the following for Part (2), $21,000 in 2004, $21,000 in 2005, $21,000 in
2006, $21,000 in 2007, $21,000 in 2008, $21,000 in 2009. Upon completion of work, the City of Palo
Alto will pay USGS $62,000 in April 2005, $62,000 in April 2006, $62,000 in April 2007, $62,000 in
April 2008, $62,000 in April 2009, and $62,000 in April 2010.
5. Additions made to the existing Statement of Work are attached as pages numbered 1 through 33.
6. All other terms and conditions of the original agreement remain unchanged.
UNITED STATES
DEPARTMENT OF THE INTERIOR
U.S. GEOLOGICAL SURVEY
(Signature)
Steven E. Ingebritsen
(Name)
_Chief~ Branch of Regional Research~ WR
(Title).~’% /.~ -~ [ ~ ~:~ ~?
Date:~/ ~" ~7 ~ ~¢~
Sro Asst. City Attorney
By:
(Signature)
(Name)
(Title)
Date:
STATEMENT OF WORK FOR THE CITY OF PALO ALTO;
NEAR FIELD RECEIVING WATER MONITORING
January 1, 2007 through December 31, 2009
U.S. Geological Survey
Samud Luoma and Janet Thompson
345 MIDDLEFIELD RD. MS 496
MENLO PARK, CA 94025
COMBINED PROPOSAL TO THE C~TY OF PALO ALTO:
NEAR FIELD RECEIVING WATER MONITORING
January 1~ 2007 through December 31~ 2009
U. S. GEOLOGICAL SURVEY
Samuel Luoma and Janet Thompson
345 MIDDLEFIELD ROAD
MENLO PARK, CA 94025
Table of Contents
Executive Summary
Tissue and Sediment Proposal
Introduction
Objectives
Monitoring Program Approach
Budget
Benthic Community Proposal
Introduction
Objectives
Approach
Budget
3
5
6
9
10
19
2O
21
23
25
33
Executive Summary of Past Findings
Since 1976, USGS personnel have assessed trace metal concentrations in sediments and
sediment-dwelling species and have profiled benthic community structure in the vicinity of the
discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP). Ancillary
factors that could affect metal concentrations (body weight in animals; characteristics of
sediment, salinity) and benthic community structure (exotic species invasions, pelagic food
availability, and weather anomalies) have also been measured during this time. These studies
initially found exceptionally high concentrations of copper and silver in mud-dwelling animals
from this area and strong seasonal variability in concentrations that confounded some
interpretations. Additional studies documented that these contaminants were present in enriched
concentrations throughout the food web, including birds from the area. The two metals that were
enriched at this site reached levels unprecedented in the literature for such species and the levels
were much greater than seen elsewhere in the Bay: annual mean concentrations for copper and
silver in clams were 287 gg/g and 105 gg/g respectively, in 1980. During this period of enriched
metal concentrations, reproductive activity in the clam being monitored for metals was very low;
this pattern is believed to be due to silver inhibition of reproductive tissue development. The
benthic community also showed signs of environmental stress during this time. The community
was dominated by opportunistic animals (organisms capable of fast invasion and spread in
disturbed environments) that lived on the surface of the mud in tubes or as shelled animals,
brooded their young, and fed on waterborne particles.
Concentrations of copper and silver declined after 1981, as the PARWQCP improved its
waste treatment facilities, in both sediments and clams. The downward trends in copper content
of animals correlated with reduced Cu discharges from the PARWQCP. The mudflat
environment where these animals live is quite complex and variable from year-to-year; but over
a long period of time (the 25 years of this study) it was obvious that there was no unidirectional
trend in any environmental factor that might explain metal concentrations, metal effects, or
benthic community changes. Particle size in sediment, salinity, organic content of sediment, and
other factors varied seasonally and from one year to another, but none of these factors showed
long-term trends. The only unidirectional change in an environmental factor during this period
was the decline in metal inputs from the waste treatment plant, at least until the 1990’s.
Coincident with the decline in copper and silver in the sediment and clams, the reproductive
activity of the clam greatly increased such that the periods of reproductive activity now exceed
the periods with no activity. The benthic community also responded to this changed
environment. Opportunistic species became less dominant and now there are more equally
dominant, equally persistent, non-opportunistic species. The community, which was previously
dominated by surface dwelling, brooding species, is now composed of species with varying life
history characteristics. In particular, species that lay their eggs in the mud and feed by
burrowing through and consuming the mud, which were previously rare in the community, have
increased in abundance. The changes to the benthic community are "young" by the standards
used to measure stability in estuarine benthic communities and patterns that are barely visible
now may become more apparent in the future.
After a minimum concentration in 1991, copper and silver concentrations in clams
increased slightly in the mid-1990’s (annual maximum concentrations were -100 gg/g for Cu and
12 gg!g for Ag). But after mid-1997, concentrations of these contaminants declined once more
to about half the mid-90’s concentrations, and the lowest we have observed (means of 26 gg/g
for Cu and 1.8 gg/g for Ag in 2005 (Cain et al (2005 and in prep) and Moon et al (2004)). The
concentrations in clams in 2005 were approaching those seen in almost uncontaminated
environments (e.g. Cu varied from 19 - 41 gg/g; lypical reference site values are 20 - 30 gg/g).
A concurrent study was conducted at San Jose for a few years and those results suggested that
trends in the 1990’s were driven by regional factors, not by changes at individual waste treatment
facilities. The legacy of contamination held in regional sediments appeared to be more important
than local factors. Other metal contaminants have also been monitored since the early 1990’s
(including selenium and mercury). For all metals studied, regional influences and year-to-year
differences appear to be much more important in determining exposures of bioavailable metals
to clams than does the local influence of the PARWQCP (again, when compared to studies at
San Jose).
These studies demonstrated the effectiveness of changes in waste discharges that
followed passage of the Clean Water Act in 1972. Metals were important pollutants in South
Bay in the late 1970’s through 1980’s, and local discharges were an important source of those
metals. That contamination has receded as the local facilities have reduced metal discharges.
Human experiments with such systems never end, however. Events like, (1) the ongoing salt
pond restoration which could mobilize old and new sediments and change the hydrodynamics of
South Bay, (2) the recent changes in the copper standard for South Bay by USEPA, and (3) new
technologies, consumer products, or uses that are growing rapidly and employ metallo-
nanoparticlesm are have the potential of altering the observed contamination in the system. An
important implication of our recent findings is that effects on metal contamination from these
changes have not proven to be sufficient to be detectable in the South Bay environment (after
treatment).
Recent changes in the seasonal pattern of phytoplankton growth and accumulation
(blooms) in south bay are also likely to affect and be affected by the benthic community. We
have seen a significant increase in the background levels of phytoplankton biomass in the south
bay since 1999. We have also observed a fall phytoplankton bloom in addition to the spring
bloom during many years since 1999. There are a number of possible factors contributing to
these changes in phytoplankton dynamics. Two strong possibilities include: (1) a change in
light availability due to lower suspended sediment concentrations; or (2) smaller populations of
filter feeding bivalves that normally heavily graze the phytoplankton during all periods except
early spring. But it is also likely that these changes would not be occurring if metal
contamination had not been reduced to a level that is no longer inhibiting phytoplankton growth.
The decline in metals in the south bay has created an environment that is more conducive to
healthy phytoplankton growth.
PROPOSAL TO THE CITY OF PALO ALTO:
NEAR FIELD RECEIVING WATER MONITORING
OF TISSUES AND SEDIMENTS:
January 1, 2007 through December 31, 2009
U. S. GEOLOGICAL SURVEY
Samuel Luoma, Daniel Cain, Michelle Homberger,
Alison Lorenzi, Janet Thompson,
Francis Parchaso
MAIL STOP 465
345 MIDDLEFIELD ROAD
MENLO PARK, CA 94025
INTRODUCTION
In the 1990’s the Regional Water Quality Control Board described a Self Monitoring
Program with its NPDES permits for South Bay dischargers that included specific receiving
water monitoring requirements. One of the requirements was for inshore monitoring of metals
and other specified parameters, to be conducted using the clamMacoma balthica and sediments,
following protocols compatible with the Regional Monitoring Program. Monitoring efforts were
to be coordinated with the U. S. Geological Survey (USGS). The latter requirement stemmed
from the 18 years of previous data that USGS collected from a station south of the Palo Alto
discharge site in the extreme South Bay. Over the last decade such a program has continued with
the partial support of the City of Palo Alto. The goal of the Board was to take advantage of that
data in interpreting monitoring data in the future. The program has had demonstrated successes
in this regard, documenting a progressive reduction of contamination at a mudflat near the
discharge of the Palo Alto RWQCP and identifying regional and local factors contributing to
more complicated trends that have occurred in recent years. The present proposal describes a
continued program of exposure monitoring at the near field (inshore) site in Palo Alto, taking
advantage of the 25 years of existing data. We also propose, in a separate document, to
accompany evaluations of trends in metal exposure with determinations of effects on
~eproduction in the indicator clam, and an evaluation of benthic .community structure. The
reproductive index and the biointegrity index are proven indicators (Homberger et al, 2000).
Monitoring these indices will allow a strong near field evaluation of environmental change in the
years ahead that is compatible with the Regional Monitoring Program’s broader approach.
1.t P~VIOU$ ~VIONITORiNG STUDIES IN NEAR FIELD RECEiIVING WATERS
Since 1976, USGS personnel have monitored and studied trace metal concentrations in
sediments and sediment-dwelling species in the vicinity of the discharge of the Palo Alto
Regional Water Quality Control Plant (PARWQCP), along with ancillary factors that could
affect metal concentrations (body weight in animals; characteristics of sediment, salinity).
These studies initially found exceptionally high concentrations of copper and silver in mud-
dwelling animals from this area and strong seasonal variability in concentrations that confounded
some interpretations. Additional studies documented that contaminants were present in
enriched concentrations throughout the food web, including birds from the area. Two metals
were enriched at this site to levels much greater than seen elsewhere in the Bay: copper and
silver (annual mean concentrations in clams were 287 gg/g and 105 gg/g respectively, in 1980).
Concentrations of copper and silver, in both sediments and clams, declined after1981, as
PARWQCP improved its waste treatment facilities. The downward trends in copper content of
animals correlated with reduced Cu discharges from the PARWQCP. The mudflat environment
where these animals live is quite complex and variable from year-to-year; but over a long period
of time (the 25 years of this study) it was obvious that there was no unidirectional trend in any
environmental factor that might explain either metal concentrations or metal effects, over this
period (particle size in sediment, salinity, organic content of sediment, etc.). The only
unidirectional change in an environmental factor was the decline in metal inputs from the waste
treatment plant, at least until the 1990’s. After a minimum concentration in 1991, copper and
silver concentrations in clams increased slightly in the mid-1990’s (annual maximum
concentrations were -100 gg/g for Cu and 12 gg/g for Ag). But after mid-1997, concentrations
7
of these contaminants declined once more to about half there levels. A concurrent study was
conducted at San Jose for a few years and it suggested that trends in the 1990’s were driven by
regional factors, not by changes at individual waste treatment facilities.
These studies demonstrated effective approaches to long term monitoring. The results
suggested that sediments and local populations of clams are sensitive indicators of the response
of receiving waters to changes in metal output from a discharger. They illustrated that reducing
metal discharge in South Bay can be reflected within a year by reduced near field
contamination in the environment and biota of San Francisco Bay. Both sediments and clams
responded sensitively to the changes. Both also incorporated important environmental factors in
their responses. When sediments and clams were monitored together, they provided
corroborating lines of evidence, minimizing mis-interpretations. The most effective
interpretation of trends occurred when samples were collected at several times of year, because
of seasonality in concentrations. The data from a receiving water monitoring program of this
type is not only useful for the Regional Board but can provide valuable feedback to local
industries and small businesses. Palo Alto has used the data to provide feedback to participants
in their silver source control program, for example. Periodically summarizing the long term data
set may offer opportunities to evaluate influences of the PAWRQCP on contamination in South
Bay compared to influences of other inputs.
By analyzing archived animals we also have recently shown that clams with high metal
exposures in the 198 O’s were unable to produce mature gametes (i. e. it is highly likely individual
animals at Palo Al~o could not reproduce)~ Archived sediment sample exist from which it can be
determined whether this affected the abundance of this animals and!or whether more sensitive
animals may have been eliminated. In the attached proposal we are suggesting to extend the
reproductive study into the future and to analyze the historic community data for effects on other
species. If those effects exist we will extend that program into the future as well. This will
provide a program of exposure and effect monitoring, consistent with risk assessment paradigms.
2.1) Objectives
The purpose of the monitoring program is to characterize long term trends in trace
element concentrations inshore near the discharge of the PARWQCP. Trace elements and
associated parameters will be determined in fine-grained sediments and in the clamMacoma
balthica. The monitoring will be conducted in a manner that will provide high-quality data that
are compatible with data collected historically, and with data provided by programs such as the
Regional Monitoring Program.
Specific objectives include:
Provide data to assess seasonal and annual trends in trace element concentrations in
sediments and dams near the discharge; specifically at the site designated in the
RWQCB’s Self-Monitoring Program for PARWQCP.
Present the data within the context of historical changes inshore in South Bay and within
the context of on-going monitoring of effluents.
, Coordinate sampling efforts with similar inshore receiving water monitoring programs
associated with the Regional Monitoring Program.
Provide data which could support other South Bay issues or programs such as
development of sediment quality standards.
The monitoring approach described below has been effective in the past in relating
9
changes in near field contamination in San Francisco Bay to changes in metal discharges from
RWQCPs, despite the complexities of monitoring natural systems. Existing historical data will
provide a context within which cause and effect can be assessed for change in the future. If
continued, this study will provide a unique opportunity to understand how investments in sewage
treatment actually affect a receiving water environment. The monitoring effort also will act as a
local extension of the Regional Monitoring Program.
3o(~ Monitoring Program Approach
The proposed approach will be to monitor trace element concentrations in fine grained
sediments and resident populations of the deposit feeding clam Macoma balthica. Sediment
particles bind most trace element pollutants strongly, efficiently removing them from the water
column. Numerous prior studies have shown that analysis of concentrations of these pollutants
in sediments provide a time-integrated indicator of trace element input to the water column.
Animals such as Macoma balthica live in contact with sediments and feed upon organic material
associated with sediment particles. Thus they are exposed to this concentrated pool of trace
elements and sequester them in their tissues. These animals are important prey for larger species
that live in the Bay, including migrating water fowl. Analysis of the tissues of the clams
provides a measure of their exposure to bioavailable pollutants and an estimate of food chain
exposures. Study of such exposure is the first step in understanding whether pollutants are
adversely affecting an environment (although elevated tissue concentrations alone do not prove
an effect is occurring). Understanding exposure in one species can be useful in indicating a
larger exposure of the local food web, as shown in earlier studies at Palo Alto. Past USGS
monitoring efforts have demonstrated the value of the dual sediment/tissue approach, when data
are collected following the rigorous protocols described below.
3.1 Sampling Design
3.1.1 Sampling location
Samples will be collected from one station located north of Sand Point (Figure 1). This is
a mudflat on the shore of the bay (not a slough) 1 kilometer south of the Palo Alto discharge. It
was chosen because it is influenced by the discharge of PARWQCP’s, but it is not immediately
adjacent to that discharge. Thus it reflects a response of receiving waters to the effluent, beyond
just a measure of the effluent itself. Earlier studies have shown that dyes, natural organic
materials in San Francisquito Creek and wasters in the PAWQCP discharge all move
predominantly south toward Sand Point and thereby influence the mudflats in the vicinity.
Earlier work showed that San Francisquito Creek and the Yacht Harbor were minor sources of
most trace elements compared to the PARWQCP. Earlier studies also showed that intensive
monitoring at one site was more effective in determining trends in trace element contamination
than was less frequent sampling at a larger number of sites in the vicinity of the discharge.
3.1.2 Sampling frequency
The basic monitoring program supported by Palo Alto will have a sampling frequency of
three times per year as stipulated by the RWQCB. Sampling will correspond as closely with
Regional Monitoring Program sampling as tides permit. The RMP samples once during the wet
season, once during the dry season and then again at the end of the dry season. The basic
program will follow this schedule also. Statistical techniques such as power analyses indicate
11
that three samples per year will provide a 20 percent sensitivity in detecting trends. The USGS
monitoring experience through the last 25 years indicates that three samples per year will be
insufficient to sensitively track seasonality in metal contamination; and that understanding the
seasonal cycles in metals and sediments is critical to understanding and interpreting metal
concentrations and their effects. The City of San Jose also now has an extensive data set on
metals in solution that further verifies that a complex seasonal cycle exists in metal
concentrations in the Bay. Thus, frequent sampling is essential to provide accurate interpretation
of cause and effect in a temporally variable environment (accuracy is not considered in power
analysis). USGS activities will include collecting samples an additional 3 - 5 times per year at
their own expense.
3.2 Constituents to be Determined
The constituents to be analyzed in sediments, and associated variables, are listed in Table ¯
1. The constituents and variables to be determined in clam tissues are listed in Table 2. The
constituent list is consistent with the constituents analyzed by the Regional Monitoring Program.
The methods employed will be adjusted so as to minimize below detection limit determinations.
The variables chosen for determination are those required by the Regional Board.
3.3 Methods
3.3ol Sampling
Macoma balthica and sediments will be collected at low tide from the exposed mudflat.
Sediment samples will be scraped from the surface oxidized layer (<2cm depth) with a metal-
free tool in a manner similar to previous sediment sampling in the area, Sediment will be
collected from the same area as the clams. Enough sediment will be obtained to conduct all
proposed analyses (Table 1) and to archive approximately 10 grams for any unforeseen future
needs. Approximately 40 individual clams will be collected at each sampling time.
3.3.2 Sample preparation
Sediments will be sieved through 100 t~m mesh in ultra-clean (-18 Mohm) deionized
water immediately upon return to the laboratory. Both the fraction of sediment passing through
the sieve and the fraction retained on the sieve will be dried and weighed. Particle size
distribution will be defined as the proportion of the total sediment mass divided between these
two fractions. This also provides an estimate of the particle size characteristics of the bulk
sediment for those who might want to make comparisons with bulk analyses.
Replicate aliquots of the fraction of sediment that passes through the 100 gm sieve will
be digested by reflux with concentrated nitric acid to determine near total concentrations (the
same approach employed by the RMP). Replicate aliquots of each sediment will also be
extracted in 0.SN hydrochloric acid to determine the leachable, anthropogenic contribution to the
sediment concentration. Standard reference materials will be digested with each sediment
digestion run.
Clams will be returned to the laboratory live, washed free of local sediment and placed in
clean ocean water diluted with distilled water to the salinity on the mudflat at the time of
collection (determined from the water in the mantle cavity of representative individual clams).
The animals will be held for two days to depurate undigested sediment, then prepared for
analysis. The length of each clam will be determined then the shell and soft tissue will be
separated. Soft tissues will be composited into 4 - 8 composite samples, each containing animals
13
of similar shell length, and digested by nitric acid reflux. Samples for mercury and selenium
analysis will be composited as above, and freeze dried before digestion in concentrated
nitric/perchloric acid. The above procedure will result in 4 - 8 replicate samples from each
collection for ICP analysis and 4 samples for mercury/selenium analysis. The data from these
animals are not normally distributed and may be affected by animal size. Correlations will be
calculated between animal size and metal concentration; and established procedures will be
employed to calculate metal content of a standard sized clam for each collection. Previous
studies show that such data reduction procedures are necessary to account for biological factors
(size and growth) that affect metal concentrations, thus allowing a clearer linkage between
RWQCP discharges and responses of the clams..
3.3.3 AnaIylical methods
Digested tissue and sediment samples will be evaporated to dryness and reconstituted in
0.6N hydrochloric acid. Most elements will be analyzed by Inductively Coupled Plasma
Emission Spectroscopy (ICP or ICAPES) (Table 1 and 2). Exceptions will include cadmium and
silver in sediments, which occur at low concentrations and will be determined by Graphite
Furnace Atomic Absorption Spectrophotometry (GFAAS) with Zeeman background correction.
The standard additions technique will be employed as necessary in these analyses.
All glassware and field collection apparatus will be acid washed, thoroughly rinsed in
ultra-clean deionized water, dried in a dust-free positive pressure environment, sealed and stored
in a dust free cabinet. Quality control will be maintained by frequent analysis of blanks, analysis
of National Institute of Standards and Technology standard reference materials (tissues and
sediments) with each analytical run, and internal comparisons with prepared quality control
standards. A full QA/QC plan is available upon request. Typical detection limits for each
element, in the matrix we are sampling, are shown in Table 3 and compared to "background" (the
lowest) concentrations found in San Francisco Bay.
3.4 Data Analysis
Data will be summarized and reported to Palo Alto annually. Annual reporting will be
consistent with Regional Monitoring Program reporting format and will be coordinated with the
receiving water monitoring programs of San Jose/Sunnyvale. Data appendices Will be included
that show basic analytical and computational data. The data report will include interpretive
figures and tables that express each year’s monitoring data within the context of historical change
and concentrations observed elsewhere.
4.~) Budget
The budget for the proposed project is outlined in detail in Table 4. This budget includes
charges only for the basic monitoring program of 3 collections per year. USGS will complement
the study with the additional collections in each year. This proposal describes work that will
begin January 2007 and continue for three years, through December 2009. Renewal each
January will be at the discretion of Palo Alto.
15
Table 1. Activities, cons¢ituents and variables ~n near field monitoring of fine grained
sediments near Palo Alto RWQCP discharges.
Activity
Schedule
Field Collections
Sediment - Particle size
Sediment - HC1 + Total
A1
Fe
Mn
Cr
Cu
Pb
Ni
Zn
Sediment - HC1 + Total
Cd
Sediment - Hg & Se (total)
TOC
Archive sediment
Assemble data
Annual Report
Method
Intertidal
>100 gm &
<100 grn
ICP
GFAAS
Hydride
Total C - GD
Scint vial
Common
spreadsheet
Common format
Additional
activities
Logistics
sieve from field
Extract or digest
Use above
extracts
Freeze dry,
grind
dry aliquot
dry
Frequency
6-8/y
6-8/y
6-8/y
6-8/y
6-8/y
3/y
6-8/y
6-8/y
6-8/y
Table 2. Activities, constituents and variables in near field monitoring of metals in the
bivalve~ Macoma balthica near the discharge of the Palo Alto RWQCPs.
Activity
Field Collect
clean, depurate,
dissect, size, dry,
weigh
Whole Tissues
Fe
Cd
Cr
Cu
Pb
Ni
Ag
Zn
Whole Tissues
Se
Condition
index/coment
Assemble data
Annual Report
Method
ICP metals
Se
As above
ICP
Hydride
Calculate
Common spreadsheet
Common Format
Additional
20 individuals
20 individuals
as above
digest etc
freeze dry,
Frequency
6-S/y
3/y
6-S/y
6-8/y
3/y
17
Table 3. Detection limits for constituents ~o be de~ermined in monitoring study (units are
micrograms per gram dry sediment).
Element Detection Background in SF Bay*
Cd 0.05 0.2
Cr 1.0 >50
Cu 1.0 10-20
Pb 1.0 5-20
Hg 0.1 0.1
Ni ] 10 >40
Se 0.1 0.1
Ag 0.05 0.1
Zn 1.0 >40
TOC 0.1%0.3 %lowest
*Determined from pre-1850 sediments from cores.
Table 4. 2007-2009 Budget* for Palo Alto Metals Studies, in dollars.
ACTIVITY SALARY SUPPLIES
Field Work 3,850 500
Sample Preparation 4,950 1,100
ICP Analyses 2,200 1,100
Mercury/Selenium
ANALYSES
2,600
Total Organic Carbon
Reduce & Assemble Data 3,465
Instrument Repair &
Maintenmlce
Final Report
SUBTOTALS
TOTAL DIRECT COST
INDIRECT COST
TOTAL COSTS 201)7
TOTAL COSTS 2008
TOTAL COSTS 2009
TOTAL COSTS 2007 through 2009
4,200
18,665 2,700
805
3,405
MISCELLANEOUS
1,650
1,650
26,420
14,580
41,1)01)’
41,000
41,000
123~000
19
PROPOSAL TO THE CITY OF PALO ALTO:
NEAR FIELD RECEIVING WATER MONITORING
OF BENTHIC COMMUNITY:
January 1, 2007 through December 31, 2009
U. S. GEOLOGICAL SURVEY
Janet K. Thompson and Francis Parchaso
MAIL STOP 496
345 MIDDLEF12ELD ROAD
MENLO PARK, CA 94025
INTRODUCTION
Concurrent, and prior to the initiation of the Luoma study, the USGS has been collecting
benthic (sediment dwelling animals) community data at three, nearby intertidal sites (south of
Sand Point). This data provides us with the opportunity to examine if the changes seen in the
tissue concentrations of metals in Macoma balthica are reflected in physiological changes to the
clams (i.e. reproduction) and are reflected in changes to the benthic community structure. In
addition, this data can serve as background information should changes to the system occur with
salt pond restoration in South San Francisco Bay. This proposal describes a continuation of the
near-field (inshore) monitoring program at Palo Alto to continue an analysis of the benthic
community between January 1, 2007 and December 31, 2009, and for analysis of reproductive
activity from January 1, 2007 through December 31, 2009.
PREVIOUS NION1TORING OF THE BENTHIC COMMUNITY IN NEAR FIELD
RECEIVING WATERS
Since 1974, USGS personnel have monitored and studied the benthic community and
reproductive activity ofMacoma balthica in the vicinity of the discharge of the Palo Alto
Regional Water Quality Control Plant (PARWQCP). Our findings during the first 10 years of
this study were published in Nichols and Thompson (1985a and 1985b). We found that this
community was composed of non-indigenous, opportunistic species that dominated the
community due to their ability to survive the many physical disturbances on the mudflat. The
disturbances discussed included sediment erosion and deposition, and exposure at e×~eme low
21
tides. The possible effects of metal exposure as a disturbance factor were not considered in these
analyses as the decline in metal concentrations inMacoma balthica and sediment had just begun.
Luoma’s results (see Homberger et al. 1999, 2000) have suggested that sediments and
local populations of clams at this location are sensitive indicators of the response of receiving
waters to changes in metal output from a discharger. These studies have illustrated that reducing
metal discharge in South Bay can be seen, within a year, as reduced near-field contamination in
the environment and biota of San Francisco Bay. Recent analysis (Thompson et al. 2002, Shouse
2002, 2003, Moon et al 2005, Cain et al 2006) has shown that the benthic community response to
reduced metal output takes longer. A response at the organism level (i.e. reproductive activity) is
seen within a year or two, but a consistent response at the community level, a change in the
number or type of species that colonized the area change when the pollutant concentration, took
several years to develop. Due to the natural intra-annual variability of benthic community
dynamics it is likely to take 5-10 years for a change in the benthic community to be stable.
Analyses of the benthic community data from 1974 thr’ough 2002 revealed the following
trends:
1.The community has shifted from being dominated by a few opportunistic species
to a community where there are more equally dominant, equally persistent
species.
2. The community, which was previously dominated by surface dwelling, brooding
species in now composed of species with varying life history characteristics.
3.Species that lay their eggs in the mud, previously rarely present in the community,
have increased in abundance.
22
4.Macoma balthica reproductive activity has increased concurrent with the decline
in tissue metal concentrations, resulting in a population with predictable semi-
annual reproductive periods.
Continued sampling and analysis will allow us to monitor if the benthic community structure
continues to reflect changes in pollutant concentration.
We propose here that samples will be analyzed at a frequency of no more than one per
month. We learned in our analyses of the early (1974 through 1983) sampling (Nichols and
Thompson 1985a, 1985b) that benthic samples need to be collected at a maximum time step of
every other month in order to distinguish seasonal differences from inter-annual differences if
the differences are small. In dynamic systems such as San Francisco Bay, distinguishing
between the effects of natural seasonal changes and anthropogenic environmental stressors is
more reliable with more f’requent samples.
Objectives
The purpose of this program is to characterize long term trends in benthic community
structure and reproductive activity ofMacoma balthica near the discharge of the PARWQCP. It
is our goal to describe these characterizations with simple measures. For example, changes in
community structure will be described as number of species, number of individuals of dominant
species and rank analysis curves (i.e. benthic communities in more polluted environments are
expected to have fewer species, and higher numbers of individuals for the dominant species than
benthic communities in non-polluted environments). Reproductive activity will be reported as
(1) total percentage of animals reproductively active for each year (we know from previous work
that this percentage is lowest during periods with the highest pollutant concentrations
23
(Homberger et al. 1999, 2000)) and (2)a reproductive index. Coincident near field monitoring of
trace element concentrations in sediment and clams (Luoma study) will allow us to compare
changes in the reproductive activity and benthic community structure with changes in metal
accumulation in animals. The analyses will be conducted in a mariner that will provide high-
quality data that are compatible with data collected historically, and with data provided by
programs such as the Regional Monitoring program.
Specific objectives are separated into two priorities and include the following:
Priori _ty 1: On-going Benthic Communi _ty Analyses (2007-2009)
® Continue monitoring to assess seasonal and annual trends in benthic community
structure at one location near the discharge (specifically at the site designated in the
RWQCB’s Self-Monitoring Program for PARWQCP)
Coordinate sampling efforts with inshore receiving water monitoring programs by
Luoma
Priority 2: Reproductive Activity ofMacoma balthica (2007-2009)
® Provide data to assess seasonal and annual trends in reproductive activity of clams near
the discharge; specifically at the site designated in the RWQCB’s Self-Monitoring
Program for PARWQCP
®Coordinate sampling efforts with inshore receiving water monitoring programs by
Luoma
The approach described below has been shown to be effective in relating changes in near
field contamination to changes in benthic community structure (Kennish, 1998) and in
reproductive activity of a clam (Homberger et al. 2000), despite the complexities inherent in
24
monitoring natural systems. Historical data (Shouse et al. 2003), provides a context for any
observed changes. Continuation of this study will build on a unique data set where ecological
data and contaminant data are concurrently collected and analyzed within the context of
changing sewage treatment practices. This monitoring effort would act as a local extension of the
Regional Monitoring Program. The coordination with Luoma’s study will provide an
environmental context for interpreting results.
Approach
The benthic community data will be analyzed in a manner similar to that used in
published benthic studies near sewage treatment ouffalls (see Kennish 1998). The proposed
approach will examine species dominance patterns and community composition changes in
combination with environmental variables. Other studies have shown that more opportunistic
species are likely to persist in highly disturbed environments (as was shown by Nichols and
Thompson (1985a) at this location in 1974 through 1983), and that the abundance and types of
dominant species can change with changes in metal concentrations (Shouse et al. 2003). We will
also examine changes in the benthic community concurrent with changes in the concentrations of
specific metals. For example it has been shown that some crustacean and polychaete species are
particularly sensitive to elevated copper (Morrisey et al. 1996, Rygg 1985) and that most
taxonomic groups have species that are sensitive to elevated silver (Luoma et al. 1995).
Analysis of the trace element concentration in the tissues ofMacoma balthica, as done by
Luoma, provides a measure of their exposure to bioavailable pollutants and an estimate of food
chain exposures. This does not however, examine the physiological effect of the metal exposure
on the animal. One of the more common animal responses to an environmental stressor is a
25
change in reproductive activity. Earlier studies (Hornberger et al 2000) have shown that
reproductive activity ofMacoma balthica has increased with declining heavy metal
concentration in animals from this location. Therefore, reproductive activity of Macoma
balthica appears to be a good indicator of physiological stress by pollutants at this location.
Sample Locations/Frequency
Samples will be collected at a station located south of Sand Point (Figure 1): station
FN45 is 12 m from the edge of the marsh and 110 cm above MLLW. The location of the benthic
station, on a mudflat on the shore of the bay (not a slough) 1 kilometer south of the Palo Alto
discharge, is influenced by the discharge of PARWQCP, but is not immediately adjacent to that
discharge. Thus this location reflects a response of redeiving waters to the effluent, beyond just a
measure of the effluent itself. Earlier studies have shown that dyes, natural organic materials in
San Francisquito Creek and wasters in the PAWQCP discharge all move predominantly south
toward Sand Point and thereby influence the mudflats in the vicinity of Sand Point (Thomson
1984). Earlier work by Luoma showed that San Francisquito Creek and the Yacht Harbor were
minor sources of most trace elements compared to the PARWQCP.
Sampling Methods
Samples for benthic community analysis will be collected quarterly from station FN45 as
part of the continuous monitoring study (Priority 1). Three replicate samples will be collected
using 8.5 cm diameter x 20 cm deep cores for the monitoring study. Our prior analysis of benthic
community data in San Francisco Bay has shown us that quarterly samples are not sufficient to
show important community patterns so the USGS will sample the benthic community an
additional two to six times per year.
26
Samples for analysis of reproductive activity will be collected on a near monthly basis
coincident with the sampling for trace elements in Macoma balthica. A minimum of 10
individual Macoma balthica of varying sizes (minimum of 5mm) will be collected for analysis.
Laboratory Analysis
Benthic community samples will be analyzed as in the past (1974-2003). Samples will
be washed on a 0.5mm screen, preserved, and 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 will be enumerated. Samples will be currated by the USGS until it can be arranged for
the California Academy of Sciences (CAS) to take this collection.
A minimum of 10 clams will be processed for reproductive activity each month. Clams
will be immediately preserved in 10% formalin at the time of collection. In the laboratory, the
visceral mass of each clam will be removed, stored in 70% ethyl alcohol, and then prepared
using standard histological techniques: tissues will bedehydrated 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 will
then be embedded in Paraplast in a vacuum chamber and then thin sectioned (10 micrometer)
using a microtome. Sections will be stained with Harris’ hematoxylin and eosin. The stained
thin Sections will be examined with a light microscope. Each individual will be 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).
27
Da~ta Analysis: Methods
Benthic community data analyses will be done at a frequency of quarterly at a minimum.
Annual patterns during prior years will be compared with the patterns seen in 2004-2009.
The seasonal benthic community data will be examined using multivariate techniques (Shouse
2002). Multivariate classification and ordination analyses will be used to identify connections
between the environmental variables (including body burdens oft race elements in bivalves and
copper and silver sediment concentrations) and benthic community structure. Data for individual
species will also be examined to determine if there are any population changes as a result of
metal concentration changes. The time series for individual species will be examined using
annual and seasonal trends, and will be examined in conjunction with time series of trace metal
concentration.. The reproductive stage data will be similarly analyzed as a time series in
conjunction with trace metal concentrations and benthic community data.
Data Analysis: Products
Data will be summarized and reported to Palo Alto at the completion of each year. Each
annual report will be consistent with the Regional Monitoring Program reporting format and will
be submitted with the Palo Alto near-field receiving water monitoring programs of Sam Luoma
from the USGS. Appendices will include species lists, species counts, species analysis by
functional group, and basic analytical and computational data for the benthic community and
reproductive data. The report will include interpretive figures and tables that show the data as a
part of the of the long-term time series. Summary, multi-year reports will include analysis of the
data within the context of the historical change of trace element concentration as reported by
Hornberger et al. (1999) and that being concurrently studied by Luoma.
28
In addition to the data report, a cartoon will be developed to demonstrate the changes
seen over the course of our study. The cartoon will be desig-ned specifically for PARWQCP’s
use for public outreach.
Budget
The budget for the proposed project is outlined in Table 1. This proposal describes work
that will begin January 2007 and continue for three years, through December 2009. Renewal
each January will be at the discretion of Palo Alto.
29
Bibliography
Cain, D.J., F. Parchaso, J.K. Thompson, S.N. Luoma, A. H. Lorenzi, E. Moon, M.K
Shouse, M.I. Homberger, J.L. Dyke, and R. Cervantes. 2005. Near field receiving water
monitoring of trace metals and a benthic community near the Palo Alto Water Quality Control
Plant in South San Francisco Bay, California: 2005. U.S. Geological Survey Open File Report
2006-1152,120 pp.
Cain, D.J., F. Parchaso, J.K Thompson, S.N. Luoma, A. H. Lorenzi, M.I. Homberger,
J.L. Dyke, and R. Cervantes. in prep. Near field receiving water monitoring of trace metals and
a benthic community near the Palo Alto Water Quality Control Plant in South San Francisco
Bay, California: 2006. U.S. Geological Survey Open File Report 2007-.
Homberger, M., S. Luoma, D. Cain, F. Parchaso, C. Brown, R. Bouse, C. Wellise, and J.
Thompson. 1999. Bioaccumulation of metals by the bivalveMacoma balthica at a site in South
San Francisco Bay between 1977 and 1997: Long-term trends and associated biological effects
with changing pollutant loadings. U.S. Geological Survey Open File Report 99-55, 42p.
Homberger, M., S. Luoma, D. Cain, F. Parchaso, C. Brown, R. Bouse, C. Wellise, and J.
Thompson. 2000. Linkage ofbioaccumulation and biological effects to changes in pollutant
loads in South San Francisco Bay. Environmental Science and Technology, 34:2401-2409.
Kennish, J.K. 1998. Pollution impacts on marine biotic communities. CRC Press, New
York. 310 pp.
Luoma, S.N., Y.B. Ho, and G. W. Bryan. 1995. Fate, bioavailability and toxicity of
silver in estuarine environments. Marine Pollution Bulletin, 31:44~54
Moon, E., M.K. Shouse, F. Parchaso, J.K. Thompson, S.N. Luoma, D. J. Cain, and M. I.
Hornberger. 2004. Near field receiving water monitoring of trace metals and a benthic
community near the Palo Alto Water Quality Control Plant in South San Francisco Bay,
Califomia: 2004. U.S. Geological Survey Open File Report 2005-1279,115 pp.
Morrisey, DJ., A.J. Underwood, and L. Howitt. 1996. Effects of copper on the faunas of
marine soft-sediments: an experimental field study. Marine Biology 125:199-213
Nichols, F.N, and J.K. Thompson. 1985a. Persistence of an introduced mudflat
community in South San Francisco Bay, California. Mar. Ecol. Prog Ser. 24:83-97.
Nichols, F.N, and J.K Thompson. 1985b. Time scales of change in the San Francisco
Bay benthos. Hydrobiologia. 129:121-138
89.
Rygg, B. 1985. Effect of sediment copper on benthic fauna. Mar. Ecol. Prog. Ser. 25:83-
30
Shouse, Michelle K 2002. The effects of decreasing trace metal concentrations on
benthic community structure. Master’s Thesis, San Francisco State University. 177pp.
Shouse M.K., Parchaso, F., and J.K Thompson. 2003. Near field receiving water
monitoring of benthic community near the Palo Alto Water Quality Control Plant in South San
Francisco Bay: February 1974 through December 2002. U.S. Geological Survey Open File
Report 03-224, 52pp.
Thomson, E.A., S.N. Luoma, C.E. Johansson, and D.J. Cain. 1984. Comparison of
sediments and organisms in identifying sources of biologically available trace metal
contamination. Water Resources. 18(6):755-765.
Thompson, J.K and F. N. Nichols. 1988. Food availability controls seasonal cycle of
growth inMacoma balthica (L.) in San Francisco Bay, California. J. Exp. Mar. Biol. Ecol.
116:43-61.
Thompson, J.K., F. Parchaso, and M.K Shouse. 2002. Near field receiving water
monitoring of benthic community near the Palo Alto Water Quality Control Plant in South San
Francisco Bay: February 1974 through December 2000. U.S. Geological Survey Open File
Report 02-394, 117pp.
31
Figm-e 1
PARWQCP~
Palo
sampling site
2 Miles
32
Table 1
Salary
$3,400
$4,700
$3,950
Analyses
$5OO
$1,000
Total
$12,050 $1,500 $13,550
$7.45O
$21,000
$21,000
$21,000
$63,000
33