HomeMy WebLinkAboutStaff Report 3514
City of Palo Alto (ID # 3514)
City Council Staff Report
Report Type: Consent Calendar Meeting Date: 4/15/2013
City of Palo Alto Page 1
Summary Title: Approval of Amendment No. 3 with the United States
Geological Survey
Title: Approval of Amendment No. 3 to Extend Contract No. C05109138 for
Three Additional Years in the Amount of $62,000 per Year for a Total of
$186,000 With The United States Geological Survey for San Francisco Bay
Monitoring
From: City Manager
Lead Department: Public Works
Recommendation
Staff recommends that Council approve and authorize the City Manager or his designee
to execute the attached Amendment No. 3 to extend Contract No. C05109138 with the
United States Geological Survey (U.S.G.S.) in the amount of $62,000 per year for a
term of three years 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.
Background
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. The work 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 (RWQCP).
Part II 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 San Francisco Bay from the RWQCP. The
sampling will cover a three-year calendar period from 2013 to 2015 and continue the
work approved by Council and completed during the previous three years
(CMR:164:10).
City of Palo Alto Page 2
Discussion
The results to date show dramatic decreases in pollutant levels in the clams compared
to the early 1980s when pollutant discharges from 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.
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 Palo Alto 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 agreemeent is $186,000. First year costs (in the
amount of $62,000) will be funded from the Wastewater Treatment Funds FY 2013
Operating budget. Future years will be subject to Council’s approval of that years
Wastewater Treatment Fund budget and the agreement acknowledges that it is
“subject to 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 (CEQA) and, therefore, an environmental assessment is not
required.
Attachments:
Attachment A: USGS Amendment 3 (PDF)
City of Palo Alto Page 3
Attachment B: Sole Source Request (DOC)
Attachment C - USGS PA Proposal 2013 final (PDF)
United States Department of the Interior
Phil Bobel
City of Palo Alto
U. S. GEOLOGICAL SURVEY
WATER RESOURCES DISCIPLINE
345 Middlefield Road
Menlo Park, California 94025·3561
Public Works Department
Environmental Compliance Division
2501 Embarcadero Way
Palo Alto, CA 94303
Dear Mr. Bobel:
February 6, 2013
Enclosed for your review and signature are two copies of Amendment 3 of Joint Funding
Agreement 04H4CAWR000010. This amendment increases the available funding by $186,000
to a new total of $744,000 and extends the period of performance to April 30, 2016.
Work performed with funds from this agreement will be billed on an annual basis. The results of
all work under this agreement will be available for publication by the USGS . Any party may
terminate this agreement by providing 30 days written notice to the other party. When an
accepted agreement is cancelled by the buyer, the seller is authorized to collect costs incurred
prior to cancellation of the agreement plus any termination costs.
After they are reviewed and signed by a party having legal authority to bind your agency, please
return one copy to our Administrative Officer, Casey Tharp, at the above address. Please retain
one original for your files.
Please contact Casey Tharp at (650) 329-4457, or via E-mail at ctharp@usgs.gov with any
questions.
Enclosure
Sincerely,
Cfff ~.
Joseph R. Holomuzki
Branch Chief
Customer #: 6000000965
Agreement#: 04H4CA WROOOOIO
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 3 for USGS Joint Funding Agreement 04H4CA WROOOOI0 (Reference Palo Alto
City Contract #C05109138) dated January 1,2004.
l. 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 frrst pmt (USGS) during the period January 1,2004 to April 30, 2016
2. Paragraph 2b ofthe agreement's funding amount is increased by $186,000 and the agreement's period
of performance is hereby extended to now read as follows:
(b) $744,000 by the party of the second part (City of Palo Alto) during the period January 1,2004
to April 30, 2016
3. The Billing Terms and Conditions listed in Paragraph 2b ofthe 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
ofthe 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,
$41,000 in 2013, $41,000 in 2014, $41,000 in 2015; 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, $21,000 in 2012, $21,000 in 2013, $21,000 in 2014, and
$21,000 in 2015. 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, $62,000 in April 2013, $62,000
in April 2014, $62,000 in April 2015, and $62,000 in April 2016.
4. All other terms and conditions ofthe original agreement remain unchanged.
UNITED STATES
DEPARTMENT OF THE INTERIOR
U.S. GEOLOGICAL SURVEY
By: -,:-:-...".",,'-L-.:-lf---'''-'--'--V----+''------f\----'''''''''"''-
(Sign
Jose
(Name)
Branch Chief
CITY OF PALO ALTO
Sr. Asst. City Attorney
By:=-:-_----:-_______ _
(Signature)
(Name)
(Title)
Date: ___________ _
. . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
City of Palo Alto
REQUEST FOR SOLE SOURCE OR EXEMPTION FROM COMPETITIVE SOLICITATION
(Purchases in excess of $5,000)
To: John Montenero Buyer or Contract Manager
From: Phil Bobel Public Works/Environmental Services Division
(Requestor) (Department/Division)
Request for the purchase of: Continued monitoring of clam tissue in San Francisco Bay adjacent to Regional Water Quality
Control Plant.
Requested supplier/vendor, if known: United States Geological Survey
Vendor Address: 345 Middlefield Road - MS 472
Menlo Park, CA 94025
Vendor Contact: Jan Thompson Phone: (650) 329-4364
Purchase Requisition #: 0000109138 0000149673 Cost Estimate $: $186K
JUSTIFICATION:
Justification must include the following:
1. A description of the unique need that requires a sole source purchase or an exemption from competitive solicitation, including why it may be impracticable, unavailing or impossible to seek bids or proposals. 2. A statement describing the actions taken by the department during the search for the product or service and the measures taken to ensure competitive pricing.
3. Any reviews, reports, or specifications prepared by the department during the research for available products or services. 4. Expected length of contract.
Provide your Justification here:
1. The United States Geological Survey (USGS) is uniquely qualified and positioned to conduct this ongoing
monitoring of the clams and clam tissue adjacent to Palo Alto’s Regional Water Quality Control Plant (RWQCP).
The USGS has been conducting this research monthly since 1974. It is imperative to execute the sampling and
analysis consistently utilizing exactly the same methods from one month to the next. Palo Alto is participating in an
ongoing program and is not paying the full cost of the monitoring. If Palo Alto were to find another “vendor”, it
would have to pay the full cost of the monitoring - a dramatic increase.
2. Knowing that no other entity is conducting clam monitoring adjacent to the Palo Alto RWQCP outfall, it would be
prohibitively expensive to contract with anyone else to do this work.
3. No such reviews or reports were done.
4. Three years.
History: We have funded the USGS research since 1994. This Sole Source request is for Amendment No. 3 to the existing Contract No. C05109138. The Regional Water Quality Control NPDES permit requires the Plant to participate in regional monitoring of metals and other specified parameters in sediments and organisms in the South San Francisco
Bay. The monitoring protocols have been designed to be compatible with or complement the RWQCB’s Regional Monitoring Program. Monitoring efforts are being conducted by the USGS and are coordinated with more than 30 years of previous data collections and investigations by the USGS at this inshore location.
Follow these Instructions for the Approval Process:
After filling out your Request, please follow these instructions: 1. The departmental approval shall be obtained by sending this Request (filled out by requestor) as an attachment via email to the Department Head, who approves by typing the words: “Request Approved”. (Any approvals required prior to this step
shall be obtained at the Department Head’s discretion and are not required as an attachment to the email.) 2. The Department Head then forwards the same email directly to the Buyer or Contract Manager assigned to the purchase
requisition. (See name at top of form.)
3. The Buyer or Contract Manager will obtain Purchasing Manager and City Manager approvals prior to processing the Request.
City of Palo Alto – Sole Source and Exemption from Competitive Solicitation
1
PROPOSAL TO THE CITY OF PALO ALTO:
NEAR FIELD RECEIVING WATER MONITORING
January 1, 2013 through December 31, 2015
U. S. GEOLOGICAL SURVEY
Dan Cain, Janet Thompson, Francis Parchaso, and Samuel Luoma
345 MIDDLEFIELD ROAD
MENLO PARK, CA 94025
2
Table of Contents
Executive Summary 3
Introduction 6
Objectives 9
Monitoring Program Approach 11
Products 17
Budget 17
3
Executive Summary of Past Findings
Since 1976, USGS personnel have assessed trace metal concentrations in sediments and
sediment‐dwelling invertebrate species and have profiled benthic community structure in the vicinity of
the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP). Ancillary
physicochemical and biological factors that influence metal concentrations in sediments, metal
concentrations in the tissues of invertebrates, 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 (Cu) and silver (Ag) in
invertebrates from this site, including the clam Macoma petalum which was being sampled at multiple
sites throughout the Bay for metal bioaccumulation studies. Additional sampling indicated that a major
source of Cu and Ag was the effluent discharged by the PARWQCP. In the mid‐1980’s, metal
concentrations in sediments and in M. petalum began to recede as source reduction/control measures
were implemented by municipal and industrial waste discharges in response to provisions under the
Clean Water Act. This period of declining metal concentrations extended into the 1990’s. Since then,
metal concentrations have remained relatively low and stable. The temporal trends in Cu and Ag copper
observed at the site corresponded with reduced Cu/Ag discharge from the PARWQCP and not with other
measured properties of the environment.
Several biological measurements indicated that infaunal species were adversely affected by the
elevated metal concentrations in the 1970‐80’s. During this period, reproductive activity in M. petalum
was low relative to after the reduction in metal concentrations. This pattern is believed to be due to Ag
inhibition of reproductive tissue development as observed in studies by other researchers. The benthic
community also showed signs of environmental stress when metal concentrations were elevated. The
community was dominated by only a few 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,
brood their young, and fed on waterborne particles. As metal concentrations receded, the composition
of the benthic community shifted to a more diverse and even distribution of species. Furthermore, the
community, which was previously dominated by surface dwelling, brooding species, shifted to its
present composition 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
4
rare in the community, 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. The biological responses described above were
most strongly correlated with the reduction in metal concentrations. Analysis of other factors that
potentially influenced species abundance such as sediment composition (for example, mean particle size
and organic content) and salinity did not correspond to the long‐term patterns that were observed. 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 and the corresponding metal concentrations in
sediments and in the bioindicator, M. petalum.
The long‐term, continuous data collected from the site presents a detailed record of the
recession of metal contamination and the subsequent recovery of the benthic invertebrate assemblage
which can be attributed to the reduction of metals loadings to South Bay achieved by PARWQCP.
Programs to control and reduce loadings of priority pollutants, including, Cu, Ag, Ni, and Hg to South Bay
and monitoring of those pollutants continue. By monitoring metal concentrations and community
dynamics, this study supports the self‐monitoring and reporting programs of PARWQCP, and
compliments the Regional Monitoring Program. In addition to providing an historical perspective and
current status of environmental conditions in South Bay, data from this study are constructing a
contemporary baseline to identify future perturbations to the benthic community. 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, and (2) new technologies, such as the rapidly expanding
commercialization of consumer products utilizing metal‐based 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.
Other changing environmental conditions will also shape ecological patterns in South Bay. For
example, recent changes in the seasonal pattern of phytoplankton growth and accumulation (blooms) in
South Bay are 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
5
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. It is also likely that these changes would not be
occurring if metal contamination was sufficient to inhibit phytoplankton growth.
6
1.0 Introduction
In the 1990's, the California Regional Water Quality Control Board (RWCB) 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 clam Macoma petalum, formerly 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 ongoing U. S.
Geological Survey (USGS) research program. 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. Since 1994, such a program has continued with the partial support of the City of Palo Alto.
The goal of the RWQB and the City of Palo Alto 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
Regional Water Quality Control Plant, identifying regional and local factors contributing to more
complicated temporal patterns, and continuing monitoring priority pollutants, including copper, nickel,
and mercury.
Concurrent with, and prior to the initiation of the metals monitoring study, the USGS also
collected benthic (sediment dwelling animal) community data at three, nearby intertidal sites south of
Sand Point). These data provided the opportunity to examine whether the changes observed in the
tissue concentrations of metals in Macoma petalum correlated with biological effects. Specifically,
reproduction in M. petalum and changes to the benthic community structure were analyzed. Indeed,
results demonstrated a strong linkage between metal exposures and biological responses at the site.
Looking forward, our understanding of water quality and the ecosystem needs to consider on‐
going and planned activities that could influence metals and biological communities in South Bay. For
example, the South Bay Salt Pond Restoration Project is nearing completion of the physical restructuring
of the ponds (expected to be completed in 2013). Remobilized sediment and water from these ponds
has been transported throughout South Bay, and likely to our field site. The potential of these newly
created habitats to be sources of metals, such as Hg, is currently being studied. In addition, recent
increases in phytoplankton biomass in South Bay since 1999 (Cloern and others, 2007) and the apparent
causes of the increase (influx of predators on the benthos and decreased turbidity) are likely to be
7
reflected in the benthic community structure if the higher phytoplankton biomass persists. Analysis of
community structure will identify long‐term shifts in species composition as well as episodic
disturbances. Monitoring of metals will contribute to a strength‐of‐evidence approach to assess
potential causes for observed changes in community structure.
The present proposal is for the three‐period starting on January 1, 2013 and ending on
December 31, 2015. The proposal describes a continuation of the near‐field (inshore) monitoring
program at Palo Alto that builds upon a long‐term record spanning 3 decades. We propose to
accompany evaluations of trends in metal exposure with determinations of biological processes that
integrate and respond to environmental perturbations on different temporal scales. Specifically,
reproduction in the indicator clam, M. petalum, and a benthic community structure will be assessed.
Monitoring metal concentrations and biological endpoints will provide a robust evaluation of site‐
specific ecological condition that is compatible with the Regional Monitoring Program’s goals (RWQB).
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, copper and silver, were especially enriched at this site compared to other
locations in the Bay.
Concentrations of copper and silver declined in both sediments and M. petalum after 1981 as
the PARWQCP implemented advanced treatment of influent and source control programs. 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
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
8
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
µg/g Cu and 4 µg/g Ag. Annual variations in tissue metal concentrations of relatively small magnitude
occur, but there have been no sustained trends and the temporal patterns no longer do not correlate
with Cu and Ag discharged from the plant. Although effluent from the plant contributes to the metal
loading to South Bay, the data suggest it does not have the predominant influence on metal
concentrations at the monitoring site that it did historically. Seasonal fluctuations and annual variation
in metal concentrations now are more likely related to a combination of factors such as local inputs,
diffuse and periodic inputs (e.g., storm related run‐off), remobilization/recycling of legacy
contamination of Bay sediments, and local physicochemical conditions affecting metal bioavailability.
Since 1974, USGS personnel have also monitored and studied the benthic community and
reproductive activity of Macoma 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 extreme low 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 balthica
and sediment had just begun.
Results from the metal study (see Hornberger and others, 1999, 2000) suggested that sediments
and local populations of clams at this location are sensitive indicators of metal loadings to nearby of
receiving waters. These studies illustrated reduced metal concentrations in sediments and in biota (M.
petalum) within a year of significant reductions in metal loading from the PARWQCP discharge. Other
analyses (Thompson and others, 2002, Shouse 2002, 2003, Moon and others, 2005, Cain and others,
2006) indicated that higher‐level biological responses metal loading take 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 a minimum of 5‐10 years for a change in the benthic
community to be stable.
9
Analyses of the benthic community data from 1974 through 2009 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.
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.
These studies demonstrated how coordinated monitoring of metals exposure and biological
response can strengthen interpretations of causality. The strong temporal associations among metal
loading, environmental levels of metal contamination, and biological responses support an
interpretation of biological recovery following a recession of metal exposures resulting from reductions
in metal loadings to South Bay by municipal and industrial dischargers in general, and PARWQCP in
particular. Temporally intensive sampling (multiple months per year) facilitated identification of long‐
term trends from annual and intra‐annual variation driven by climate patterns and growth and
reproductive cycles in benthic invertebrates. 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 dischargers.
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.
2.0 Objectives
The purpose of the monitoring program is to characterize temporal trends in trace element
concentrations, the reproductive activity of the bioindicator, M. petalum, and the benthic community
structure inshore at a site near the discharge of the PARWQCP. Specifically, trace elements and
associated parameters will be determined in surficial, fine‐grained sediments and in the clam M.
10
petalum, the reproductive state of M. petalum will be evaluated, and the structural and functional
features of the benthic community will be analyzed. Biological attributes will be characterized with
simple, established metrics. Reproductive activity will be reported as 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 (Hornberger and others, 1999, 2000)) and as a
reproductive index. Community composition will be described in terms of 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). All 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 Program.
Specific objectives include:
1. 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.
2. Present the data within the context of historical changes inshore in South Bay and
within the context of on‐going monitoring of effluents.
3. Coordinate sampling efforts with similar inshore receiving water monitoring programs
associated with the Regional Monitoring Program.
4. Provide data which could support other South Bay issues or programs such as
development of sediment quality standards.
5. 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)
6. 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
Despite the complexities of monitoring natural systems, 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. We have been also been effective in relating changes in
11
near field contamination to changes in benthic community structure (Kennish, 1998) and in reproductive
activity of a clam (Hornberger and others, 2000). 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
data on metal concentrations in the local receiving water that can be evaluated within the context of
similar data collected by Regional Monitoring Program), feed‐back on new or on‐going initiatives to
control and mitigate inputs of metals from sources within the service area, and new treatment
technologies to reduce effluent loadings. 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. In addition, USGS will provide material support to the City of
Palo Alto for the creation of a self‐guided path within the Baylands Nature Preserve that illustrates the
ecological recovery of the intertidal site following the reductions in metal loadings to South Bay.
3.0 Monitoring Program Approach
The proposed approach will 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. Uptake of trace elements
from ingested sediments results in their accumulation in the tissues of M. petalum. These animals are
important prey for larger species that live in the Bay, including migrating waterfowl. Thus, analysis of
the tissues of the clams provides a measure of their exposure to bioavailable pollutants and an estimate
of their food web transfer of the pollutants.
Analysis of the trace element concentration in the tissues of a bioindicator, such as M. petalum,
indicates whether a pollutant is bioavailable and bioaccumulated. Although elevated pollutant
concentrations in an organism suggest an increased probability of toxicological risk, it does not confirm
toxicity. Chronic metal toxicity in an invertebrate can manifest in physiological impairment, including
reproductive impairment (Hook and Fisher 2001a; 2001b) and retarded growth (Irving and others,
2003). Annual growth and reproductive cycles in M. petalum can be followed with the condition index
(CI), which is an indicator of the physiological condition of the animal and, specifically, is the total soft‐
12
tissue weight of a clam standardized to shell length (Cain and others, 1990). Earlier studies of M.
petalum from the site near the PARWCQP outfall showed that reproductive activity increased as Cu and
Ag concentrations in the clam’s soft tissues declined (Hornberger and others, 2000). Therefore, the CI
and reproductive activity of M. petalum appears to be a good indicators of physiological stress related to
elevated exposure to some metals, at least.
The benthic community data will be analyzed in a manner similar to that used in published
benthic studies near sewage treatment outfalls (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 and others, 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 and others, 1996, Rygg 1985) and that most taxonomic groups have species that are sensitive
to elevated silver (Luoma and others, 1995).
3.1 Sampling Design
3.1.1 Sampling Location
Samples for sediment and clam tissue metal concentrations will be collected from one station
located south of Sand Point (Figure 1). Benthic community samples will be collected at a station located
near Sand Point (Figure 1): station FN45 is 12 m from the edge of the marsh and 110 cm above MLLW.
These locations are on 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 of
PARWQCP, 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 PAWQCP 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
13
larger number of sites in the vicinity of the discharge.
3.1.2 Sampling Frequency
The basic metals monitoring program supported by Palo Alto will have a sampling frequency of
three times per year as stipulated by the RWQCB. 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. Sampling will correspond as closely with Regional Monitoring Program sampling as tides
permit. Statistical techniques such as power analyses indicate that three samples per year will provide
20 percent sensitivity in detecting trends. The USGS monitoring experience at the site indicates that
seasonal cycles and episodic events influence annual variation in metal concentrations in sediments and
tissues; three samples per year will be insufficient to track and characterize seasonality in metal
contamination. Consequently, important episodic events may be missed, associations between metals
and biological metrics, such as community structure, are weakened, and long‐term trends in both metal
exposure and community composition are more difficult to define. Thus, samples will be collected more
frequently as stipulated below.
To support interpretations of cause and effect in a temporally variable environment, metal and
benthic invertebrate sampling should be coincident and thus sampling will coincide with the three
periods stipulated by the RWQCB. In addition, previous analyses of benthic invertebrate data (1974
through 1983) indicated that benthic samples need to be collected at a time step of about every other
month in order to distinguish seasonal differences from inter‐annual differences if the differences are
small (Nichols and Thompson 1985a, 1985b). 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. Thus, the USGS will sample metals in the
sediment and clam tissue and will sample the benthic community an additional two to six times per
year.
3.2 Constituents to be Determined
The chemical constituents to be analyzed in sediments and in the tissues of M. petalum as well
as ancillary chemistry and physical properties are listed in Table 1. The constituent list is consistent with
the chemical and physical constituents analyzed by the Regional Monitoring Program. The methods
employed are designed to minimize below detection limit determinations. The variables chosen for
determination are those required by the Regional Board.
14
Benthic samples will be processed to produce species lists, species counts, and species
functional group. Each clam selected for reproductive analysis will be characterized by size (length in
mm), sex, developmental stage, and condition of gonads.
3.3 Methods
3.3.1 Sampling
Sediments and M. petalum will be collected at low tide from the exposed mudflat. Sediment
samples will be scraped from the visibly oxidized (brownish) surface layer (top 1–2 cm) of mud. This
surface layer represents recently deposited sediment and detritus, or sediment affected by recent
chemical reactions with the water column. The sediment also supports microflora and fauna, a
nutritional source ingested by M. petalum. Enough sediment will be obtained to conduct all proposed
analyses (Table 1) and to archive approximately 10 grams for any unforeseen future needs. Clams will
be collected by hand from the same area. Typically, 60–120 individuals will be collected, representing a
range of sizes (shell length). As they are collected, the clams will be placed into screw‐cap polypropylene
container (previously acid‐washed) containing site water. These containers will be used transport the
clams to the laboratory.
Three replicate samples will be collected using 8.5 cm diameter x 20 cm deep cores for the
benthic community monitoring study. A minimum of 10 individual Macoma balthica of varying sizes
(minimum of 5mm) will be collected for the analysis of reproductive activity.
3.3.2 Sample Preparation
Sediments will be sieved through 100 μm 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 μm 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 sediment will also be extracted in 0.5N
hydrochloric acid to determine the leachable, anthropogenic contribution to the sediment
concentration (Luoma and Bryan 1982). Another aliquot will be prepared for the determination of total
15
organic carbon following the method described by Harris and others (2001). 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). Clams will be moved to a constant temperature room (12ºC)
and starved for 48 hours to allow for the egestion of sediment and undigested material from their
digestive tracts.
Following depuration, 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, then frozen. Later, the samples will be homogenized refrozen, and then freeze
dried. Subsamples will be weighed, and then digested in concentrated nitric/peroxide. 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 to facilitate comparisons of metal exposure over time. 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 PARWQCP discharges and responses of
the clams.
Benthic samples will be washed on a 0.5mm screen, preserved in 10% formalin for two weeks
and then transferred to 70% ethyl alcohol with Rose Bengal stain. Clams collected for reproductive
analysis 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.
3.3.3 Analytical methods
Digested tissue and sediment samples will be evaporated to dryness and reconstituted in 0.6N
16
hydrochloric acid. Most elements will be analyzed by Inductively Coupled Plasma Optical Emission
Spectrophotometry (ICP‐OES) (Table 1). Selenium will be determined by Inductively Coupled Plasma
Mass Spectrometry (ICP‐MS) staged with a hydride generation unit (Kleckner, USGS, pers. commun.).
Mercury will be determined using established methods (Olund and others, 2004; USEPA, 2001). The
total carbon content of sediment samples was determined from the analysis for elemental abundance
and C using a Carlo Erba NA 1500 elemental analyzer connected to an Elementar Optima isotope ratio
mass spectrometer (Steve Silva, USGS, pers. commun.).
To minimize metal contamination of samples, all glassware and plastic used for sample
collection, preparation, and storage will be cleaned by sequentially washing with a detergent, deionized
water rinse, followed by a 10‐percent hydrochloric‐acid wash and double‐deionized water (18 mega‐
ohm (MΩ) resistivity) rinse. Materials will be dried in a dust‐free positive‐pressure environment, sealed,
and stored in a cabinet. Quality control will be maintained by frequent analysis of blanks, analysis of
National Institute of Standards and Technology standard reference materials (e.g., NIST 2709a, San
Joaquin soils, and NIST 2976, mussel tissue) with each analytical run, and internal comparisons with
prepared quality control standards. Method detection limits (MDL) and reporting levels (MRL) will be
determined using the procedures outlined by Glaser and others (1981), Childress and others (1999), and
U.S. Environmental Protection Agency (2004). A full quality‐assurance/quality‐control plan is available
upon request.
Benthic samples will be sorted and individuals identified to the lowest taxonomic level possible
(some groups are still not well defined in the bay, such as the oligochaetes), and individuals for each
species will be enumerated.
The stained thin sections of clam reproductive tissue 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 (Parchaso 1993).
3.4 Data Analysis
The period of sample collection is the calendar year. Annual data will be compiled, summarized,
and appended to the long‐term dataset. Data for sediment chemistry and metal concentrations in the
bioindicator, M. petalum, will be assessed within the context of the long‐term record as well as more
recent data. Changes in elemental constituents and associations among those constituents and with
17
other environmental properties will be analyzed by parametric and non‐parametric statistical models,
such as correlation and ANOVA.
The seasonal benthic community data will be examined using multivariate techniques (Shouse
2002). Multivariate 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 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.
4.0 Products
Data will be summarized and reported to the City of Palo Alto at the completion of each
sampling period (i.e., calendar year). Annual reports will be consistent with the Regional Monitoring
Program reporting format. Appendices will include basic analytical data and computations, quality
assurance data, species lists, species counts, species analysis by functional group, and basic analytical
and computational data for the benthic community and reproductive data. To meet the objectives of
the study, the report will include interpretive figures, tables and narrative descriptions of the most
recent data in relation to 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 (e.g., Hornberger
and others, 1999).
5.0 Budget
The budget for the proposed project is outlined in detail in Table 2. This budget includes
charges only for the basic monitoring program of 3 sediment and clam tissue collections per year and for
4 benthic community collections per year. USGS will complement the study with the additional
collections in each year. This proposal describes work that will begin January 2013 and continue for
three years, through December 2015. Renewal each January will be at the discretion of Palo Alto.
18
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22
Figure 1. Map of Palo Alto sampling site and the surrounding region. The locations where
benthic invertebrate samples and metals samples (sediments and M. petalum) will be collected are
shown in panel B.
23
Table 1. Chemical and physical data, sampling frequency (per year), and analytical methodology
proposed for monitoring the near‐field discharge of the Palo Alto RWQCP.
Constituent Matrix Frequency Method
Ag Sediment and tissue 6‐8 ICP‐OES
Al Sediment 6‐8 ICP‐OES
Cd Sediment and tissue 6‐8 ICP‐OES
Cr Sediment and tissue 6‐8 ICP‐OES
Cu Sediment and tissue 6‐8 ICP‐OES
Fe Sediment and tissue 6‐8 ICP‐OES
Hg (total) Sediment and tissue 3 Atomic fluorescence spectrometry
Mn Sediment 6‐8 ICP‐OES
Ni Sediment and tissue 6‐8 ICP‐OES
Pb Sediment and tissue 6‐8 ICP‐OES
Se Sediment and tissue 6‐8 ICP‐MS coupled to hydride generation
Zn Sediment and tissue 6‐8 ICP‐OES
Particle size Sediment 6‐8 Physical separation (>100 μm & <100 μm)
TOC Sediment 6‐8 ICP‐MS
Archive Sediment 6‐8 Dry sediment storage
24
Table 2. 2012‐2015 Budget for Palo Alto Studies.
ACTIVITY SALARY SUPPLIES ANALYSES MISC TOTALS
Sediment
& Tissue
Community
&
Reproduction
Sediment
& Tissue
Sediment
& Tissue
Community
&
Reproduction
Field Work $3,850 $3,400 $500
Sample Preparation $4,950 $4,700 $1,100
Analyses (exclusive
of mercury and
selenium)
$2,200 $1,100
Mercury/
Selenium
$2,600
Invertebrate
Taxonomy
$500
Reproductive Tissue
Processing
$1,000
Total Organic Carbon $805
Data Analysis $3,465 $2,000
Instrument
Maintenance/Repair
$1,650
Final Report $4,200 $1,950
SUBTOTALS $18,665 $12,050 $2,700 $3,405 $1,500 $1,650
TOTAL DIRECT COST/Year $39,970
INDIRECT COST/Year $22,030
TOTAL COSTS 2013 $62,000
TOTAL COSTS 2014 $62,000
TOTAL COSTS 2015 $62,000
TOTAL COSTS 2013 through 2015 $186,000