HomeMy WebLinkAboutStaff Report 146-10TO: HONORABLE CITY COUNCIL
FROM: CITY MANAGER DEPARTMENT: PUBLIC WORKS
DATE: MARCH 8, 2010 CMR:146:10
REPORT TYPE: CONSENT
SUBJECT: Approval of a Three-Year Extension to the Agreement with the United
States Geological Survey in the 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 $62,000 per year for a total 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 2010-2012.
DISCUSSION
Project Description
The work to be done by the U.S.G.S. consists of two parts. Part 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 (R WQCP). Part IT provides for monitoring of the number and diversity
of the benthic organisms and the reproductivity 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 2010 -2012), and continue the work approved by Council and completed during the
past three years (CMR:197:07).
.... ~
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 IT 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.
CMR:146:10 Page 1 of2
The Regional Board and the City wish to take advantage of the knowledge, experience, and
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 agreement is $186,000. First year costs in the amount of $62,000 will
be funded from fiscal year 2009-10 operating budget of the RW QCP. It is anticipated that funds for
the second year ($62,000) and the third year ($62,000) will be included for in subsequent base
budgets. The agreement acknowledges that it is "subject to the availability of appropriations". As
with almost all RWQCP expenditures, approximately 113 of expenditure comes from Palo Alto funds
and approximately 2/3 comes from the other partners of the Plant.
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:
-----~-------------------------PHIL BOBEL
Manager, Environmental Compliance Division
Ii 1, f:kr:
GLENN S. ROBERTS
Director of Public Works
J KEENE . .
Ci anager
Page 2
ATTACHMENT A
Customer #: CA228
Agreement#: 04H4CAWROOOOIO
TIN#: 94-6000389
Fixed Cost Agreement: Yes
UNITED STATES DEPARTMENT OF THE INTERIOR
U.S. GEOLOGICAL SURVEY
AMENDMENT OF JOINT FUNDING AGREEMENT
FOR
WATER RESOURCES INVESTIGATIONS
This is Amendment 2 for USGS Joint Funding Agreement 04H4CA WROOOOI 0 (Reference Palo 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 ofperfonnance 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, 2013
3. Paragraph 2b ofthe agreement's funding amount is increased by $186,000 and the agreement's period
ofperfonnance is hereby extended to now read as follows:
(b) $558,000 by the party of the second part (City of Palo Alto) during the period January 1,2004
to April 30, 2013
4. The Billing Tenns 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, $41,000 in 2010, $41,000 in
2011, $41,000 in 2012; 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, $21,000 in
2010, $21,000 in 2011, and $21,000 in 2012. 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, $62,000 in April 2010,
2011, $62,000 in April 2012, and $62,000 in April 2013.
5. Additions made to the existing Statement of Work are attached as pages numbered 1 to 35.
6. All other tenns and conditions of the original agreement remain unchanged.
UNITED STATES
DEPARTMENT OF THE INTERIOR
U.S. GEOLOGICAL SURVEY
,/ -/)) BY:~/J~
(Signature) ,
Keith R. Prince
(Name)
Branch Chief
(Title) /
Date: { ~; 12 u /0 I I
CITY OF PALO ALTO
Sr. Asst. City Attorney
By::::::---:----:-_______ --
(Signature)
(Name)
(Title)
Date: ___________ _
COMBINED PROPOSAL TO THE CITY OF PALO ALTO:
NEAR FIELD RECEIVING WATER MONITORING
January 1, 2010 through December 31, 2012
U. S. GEOLOGICAL SURVEY
. Janet Thompson, Dan Cain, and Samuel Luoma
345 MIDDLEFIELD ROAD
MENLO PARK, CA 94025
1
Table of Contents
Executive Summary 3
Tissue and Sediment Proposal 5
Introduction 6
Objectives 9
Monitoring Program Approach 10
Budget 19
Bent,hic Community Proposal 20
Introduction 21
Objectives 23
Approach 25
Budget 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 (PAR WQCP). 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
Macoma petalum, the clam used to monitor metals at the site, were 287 flg/g and 105 flg/g
respectively, in 1980. During this period of enriched metal concentrations, reproductive activity
in M petalum was very low. This 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 in both sediments and M petalum after
1981 as the P ARWQCP improved its waste treatment facilities .. The downward trends in copper
in sediments and in the clam corresponded with reduced Cu discharges from the P ARWQCP.
The mudflat environment where this animal lives is quite complex and variable from year-to
year. Sediment composition (for example mean particle size and organic content), salinity, and
other factors varied seasonally and from one year to another. However, over a long period of
study (32 years) none of these factors displayed sustained directional trends that corresponded to
the changes in metal concentrations, metal effects, or benthic community changes. The only
unidirectional change in an environmental factor during this period was the decline in metal
inputs from the waste treatment plant during the 1980s. 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.
Since the significant reductions in the 1980's, concentrations of Cu and Ag in sediments
and clams have remained relatively low, fluctuating modestly but without a sustained temporal
trend. For example, since 1991 copper and silver concentrations in clams averaged 40 and 3.9
3
Jlg/g, respectively. Positive excursions occurred in 1992-1996 when concentrations averaged 59
Jlg/g Cu and 6.2 Jlg/g Ag, but concentrations after this period typically ranged between 30-40
Jlg/g and 2-3 Jlg/g Ag. The lower range ofCu concentrations are comparable to the lower range
of values from other sites within the Bay (20 -30 Jlglg), and therefore could mark the approach
of a regionally-defined baseline concentration. Although Ag remains elevated it was only 3
percent of the maximum value observed in 1980. Importantly, since 1991 annual variations in
metal concentrations in M petalum do not correlate with discharge of Cu and Ag from
P ARWQCP, suggesting that variations in tissue metal concentrations due to metals discharged
from the plant can not longer be distinguished against the background of other variables .. 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. Although metal contamination of the Bay has receded as the local facilities implemented
different and better treatment technologies, human impacts on the Bay ecosystem will continue.
Events that have the potential of altering the observed contamination in the system include: (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, such as the rapidly expanding commercialization of
consumer products utilizing metallo-nanoparticles. 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 present South Bay environment
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 1,2010 through December 31, 2012
U. S. GEOLOGICAL SURVEY
Daniel Cain ,Samuel Luoma, Michelle Hornberger,
MAIL STOP 465
345 MIDDLEFIELD ROAD
MENLO PARK, CA 94025
5
1.0 INTRODUCTION
In the 1990's the Regional Water Quality Control Board described a Self Monitoring
Program with its NPDES pennits 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 clam Macoma petalum, fonnerly
reported as Macoma balthica (Cohen and Carlton, 1995), 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
temporal patterns.
Looking forward, our understanding of water quality and the ecosystem needs to consider
on-going and planned activities during the next three years. The South Bay Salt Pond
Restoration Project is about to enter an intensive period of construction and opening of ponds to
the bay. Present plans (July 2009) show one pond at Ravenswood will be breached in Aug 2010,
and two more in Alviso will be breached in September and November 2010. Remobilized
sediment and water from these ponds are likely to be transported throughout South Bay, and
specifically to our field site. In addition, recent increases in phytoplankton biomass in South Bay
since 1999 (Cloern et al. 2007) and the apparent causes of the increase (influx of predators on the
benthos and decreased turbidity) are likely to be reflected in the benthic community structure if
the higher phytoplankton biomass persists. Monitoring of metals will contribute to a strength-of
evidence approach to assess potential causes for observed shifts in community composition.
The present proposal describes a continued program of metal exposure monitoring at the
near field (inshore) site in Palo Alto, taking advantage ofthe more than 32 years of existing data.
We also propose, in a separate document, to accompany evaluations of trends in metal exposure
with determinations of effects on reproduction in the indicator clam, and an evaluation of benthic
community structure. The reproductive index and the biointegrity index are proven indicators of
biological responses to metals (Hornberger et aI, 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.
1.1 PREVIOUS MONITORING STUDIES IN NEAR FIELD RECEIVING 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
7
enriched at this site to levels much greater than seen elsewhere in the Bay: copper and silver
(mean concentrations in M. petalum were 287 Ilg/g and 105 Ilg/g, respectively, in 1980).
Concentrations of copper and silver declined in both sediments and M. petalum after
1981 as the P ARWQCP improved its waste treatment facilities. The downward trends in copper
in sediments and in the clam correlated with reduced Cu discharges from the PARWQCP. The
mudflat environment where this animal lives is quite complex and variable from year-to-year.
Sediment composition (for example mean particle size and organic content), salinity, and other
factors varied seasonally and from one year to another. However, over a sustained period of
study (32 years) none of these factors displayed temporal trends that corresponded to the changes
in metal concentrations, metal effects, or benthic community changes. The only unidirectional
change in an environmental factor during this period was the decline in metal inputs from the
waste treatment plant during the 1980s. Since 1991, metal concentrations in M petalum more or
less stabilized around 40 Ilg/g Cu and 4 Ilg/g Ag. Annual variations in tissue metal
concentrations of relatively small magnitude occur, but there have been no sustained trends and
the temporal patterns do not correlate with Cu and Ag discharged from the plant. A concurrent
study was conducted at another site in South Bay for several years, and it suggested that
temporal variation at least during the 1990s was driven by regional factors rather than discharges
at individual 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. Also, both 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 during the 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 P A WRQCP 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 1980's were unable to produce mature gametes (i.e. it is highly likely individual
animals at Palo Alto could not reproduce). In the attached proposal we are suggesting to extend
the reproductive study into the future and to continue to analyze the community data for effects
on other species, thereby providing a program of exposure and effect monitoring, consistent with
risk assessment paradigms.
2.0 Objectives
The purpose of the monitoring program is to characterize trends in trace element
concentrations inshore near the discharge of the P ARWQCP. Trace elements and associated
parameters will be determined in fine-grained sediments and in the clam M petalum. The
monitoring will be conducted in a manner that will provide high-quality data that are compatible
with existing data, and with data provided by programs such as the Regional Monitoring
9
Program.
Specific objectives include:
• Provide data to assess seasonal patterns and annual trends in trace element concentrations
in sediments and clams 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
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 build on a unique record of understanding 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.
3.0 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 M petalum. 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 M. petalum 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) approximately 1 kilometer southeast of the Palo
Alto discharge. It was chosen because it is influenced by the discharge ofPARWQCP, 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 effluent from the PA WQCP all move
11
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
that three samples per year will provide a 20 percent sensitivity in detecting trends. The USGS
monitoring experience through the last 32 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 detennined 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 detenninations.
The variables chosen for detennination are those required by the Regional Board.
3.3 Methods
3.3.1 Sampling
M. petalum 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 60 individual clams will be collected for metals analysis at each sampling
time. In addition, approximately 40 individual clams will be collected for total analysis of
mercury and selenium three times during the year.
3.3.2 Sample preparation
Sediments will be sieved through 100 Jlm 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
13
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 llm 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 O.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 oflocal 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
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 ICPOES 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 Analytical methods
Digested tissue and sediment samples will be evaporated to dryness and reconstituted in
O.6N hydrochloric acid. Most elements will be analyzed by Inductively Coupled Plasma Optical
Emission Spectrophotometry (ICPOES) (Table I and 2).
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. Detection limits for each ICPOES analytical method (tissue and sediment) are
determined. Typical detection limits for each element, in the appropriate sample matrix, are
shown in Table 3 and compared to "background" (the lowest) concentrations found in San
Francisco Bay. A full QAlQC plan is available upon request.
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 that show basic
analytical and computational data will be included. 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.
15
4.0 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 2010 and continue for three years, through December 2012. Renewal each
January will be at the discretion ofPa10 Alto.
Table 1. Activities, constituents and variables in near field monitoring of fine grained
sediments near Palo Alto RWQCP discharges.
Activity Method Additional Frequency
activities
Field Collections Intertidal Logistics 6-8/y
Sediment -Particle size >100 f.Ull & sieve from field 6-8/y
<100 11m
Sample prep for metals HCI & Total 6-8/y extractions
Sample prep for Hg & Se Hydride Freeze dry, 3/y
(total) sample shipping
Quantitative analysis ICPOES 6-8/y
(metals listed below)
Ag
Al
Fe
Mn
Cd
Cr
Cu
Pb
Ni
Zn
Hg & Se (total) Hydride 3/y
TOC Total C dry aliquot 6-8/y
Archive sediment Scint vial Dry 6-8/y
Assemble data Common 6-8/y
spreadsheet
Annual Report Common fonnat lIy
17
Table 2. Activities, constituents and variables in near field monitoring of metals in the
bivalve, Macoma petalum near the discharge of the Palo Alto RWQCPs.
Activity Method Additional Frequency
Field Collect Intertidal Logistics 6-8/y
Sample preparation metals 60-80 individuals 6-8/y
Sample preparation Hg&Se 40 individuals 13/y
Quantitative analysis ICPOES 6-8/y
(metals listed below)
Ag
Fe
Mn
Cd
Cr
Cu
Pb
Ni
Zn
Se & Hg (total) Hydride Sample packaging 3/y
and shipping
Condition Calculate
index/content
Assemble data Common spreadsheet 6-8/y
Annual Report Common Fonnat 1/y
Table 3. Typical detection limits for constituents to be determined 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 1.0 >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.
19
Table 4. 2007-2009 Budget* for Palo Alto Metals Studies, in dollars.
ACTMTY
Field Work
Sample Preparation
ICP Analyses
Mercury/Selenium
Total Organic Carbon
Reduce & Assemble Data
Instrument Repair &
Maintenance
Final Report
SUBTOTALS
TOTAL DIRECT COST
INDIRECT COST
TOTAL COSTS 2010
TOTAL COSTS 2011
TOTAL COSTS 2012
SALARY
3,850
4,950
2,200
3,465
4,200
18,665
TOTAL COSTS 2010 through 2012
SUPPLIES ANALYSES
500
1,100
1,100
2,600
805
2,700 3,405
MISCELLANEOUS
1,650
1,650
26,420
14,580
41,000
41,000
41,000
123,000
PROPOSAL TO THE CITY OF PALO ALTO:
NEAR FIELD RECEIVING WATER MONITORING
OF BENTHIC COMMUNITY:
January 1,2010 through December 31,2012
U. S. GEOLOGICAL SURVEY
Janet K. Thompson and Francis Parchaso
MAIL STOP 496
345 MIDDLEFIELD ROAD
MENLO PARK, CA 94025
21
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 petalum 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, 2010 and December 31, 2012, and for analysis of reproductive
activity from January 1, 2010 through December 31, 2012.
PREVIOUS MONITORING OF THE BENTHIC COMMUNITY IN NEAR FIELD
RECEIVING WATERS
Since 1974, USGS personnel have monitored and studied the benthic community and
reproductive activity of Macoma petalum 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 extreme low
22
tides. The possible effects of metal exposure as a disturbance factor were not considered in these
analyses as the decline in metal concentrations in Macoma petalum and sediment had just begun.
Luoma's results (see Hornberger 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 a12005, Cain et a12006) has shown that the benthic community response to
reduced metal output takes longer. A response at the organism level (Le. 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.
trends:
Analyses ofthe benthic community data from 1974 through 2009 revealed the following
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.
23
4. Macoma petalum 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 frequent samples.
Objectives
The purpose of this program is to characterize long term trends in benthic community
structure and reproductive activity of Macoma petalum 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
24
(Hornberger et a1. 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 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 are separated into two priorities and include the following:
Priority 1: On-going Benthic Community Analyses (2010-2012)
• 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 of Macomapeta/um (2010-2012)
• 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 P ARWQCP
• 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 (Hornberger et a1. 2000), despite the complexities inherent in.
25
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 outfaIls (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 aI. 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 of Macoma petalum, as done by
Luoma, provides a measure of their exposure to bioavailab1e 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
26
change in reproductive activity. Earlier studies (Hornberger et al 2000) have shown that
reproductive activity of Macoma petalum has increased with declining heavy metal
concentration in animals from this location. Therefore, reproductive activity of Macoma petalum
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 em above MLL W. 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 PAR WQCP, but is not immediately adjacent to that
discharge. Thus this location 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 P A WQCP 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.
27
Samples for analysis of reproductive activity will be collected on a near monthly basis
coincident with the sampling for trace elements in Macoma petalum. A minimum of 10
individual Macoma petalum of varying sizes (minimum of Smm) 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 O.Smm 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 be 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 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 Oength 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).
28
Data 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 of trace 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 change&. 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 appended to the existing data record maintained by the USGS, summarized,
reviewed and reported with the metals data as annual USGS Open-File Reports that will be made
available to the City of Palo Alto at the completion of each year. Each annual report will be
consistent with the Regional Monitoring Program reporting format. 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
29
change of trace element concentration as reported by Hornberger et al. (1999) and that being
concurrently studied by Luoma.
Budget
The budget for the proposed project is outlined in Table 1. This proposal describes work
that will begin January 2010 and continue for three years, through December 2012. Renewal
each January will be at the discretion of Palo Alto.
30
Bibliography
Cain, DJ., F. Parchaso, J.K. Thompson, S.N. Luoma, A. H. Lorenzi, E. Moon, M.K.
Shouse, M.I. Hornberger, J.L. Dyke, and R. Cervantes. 2005. Near field receiving water
monitoring oftrace 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.
Cloern, J.E., Jassby, A.D., Thompson, J.K, Hieb, K. 2007. A cold phase of the east
Pacific triggers new phytoplankton blooms in San Francisco Bay. Proceedings National
Academy of Science v. 104, no. 47, p. 18561-18565
Cohen, A.N., and Carlton. J.T., 1995, Biological study, nonindigenous aquatic species in a
United States estuary; a case study of the biological invasions of the San Francisco Bay and
Delta: Washington D. C., U.s. Fish and Wildlife Service.
Hornberger, M., S. Luoma, D. Cain, F. Parchaso, C. Brown, R. Bouse, C. Wellise, and J.
Thompson. 1999. Bioaccumulation of metals by the bivalve Macoma balthica at a site in South
San Francisco Bay between 1977 and 1997: Long-term trends and associated biological effects
with changing pollutant loadings. U.S. Geological Survey Open File Report 99-55, 42p.
Hornberger, 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.
Lorenzi, A., Cain, D. J., Parchaso, F., Thompson, J.K., Luoma, S.N., Hornberger, M.I.,
Dyke, J.L., Cervantes, R., and Shouse, M.K. 2007, 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: 2006: u.s. Geological Survey Open File Report 2007-1199, 121p.
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,
California: 2004. U.S. Geological Survey Open File Report 2005-1279, 115 pp.
Morrisey, DJ., AJ. Underwood, and L. Howitt. 1996. Effects of copper on the faunas of
marine soft-sediments: an experimental field study. Marine Biology 125:199-213
31
Nichols, F.N, and J.K. Thompson. 1985a. Persistence ofan 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
Rygg, B. 1985. Effect of sediment copper on benthic fauna. Mar. Ecol. Prog. Ser. 25:83-
89.
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.B. Johansson, and DJ. 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 in Macoma balthica (L.) in San Francisco Bay, California. J. Exp. Mar. BioI. 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.
32
Figure 1
Palo Alto
sa mpli ng site
33
$3,950
34
Total
$500
$1,000
$1,500 $13,550
$7.450
$21,000
$21,000
$21,000
$63,000