Publications— Open-File Reports

Near-Field Receiving Water Monitoring of Trace Metals and a Benthic Community Near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California: 2005

U.S. Geological Survey Open-File Report 2006-1152

By Daniel J. Cain, Francis Parchaso, Janet K. Thompson, Samuel N. Luoma, Allison H. Lorenzi, Edward Moon, Michelle K. Shouse, Michelle I. Hornberger, and Jessica L. Dyke

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Trace elements in sediment and the clam Macoma petalum (formerly reported as Macoma balthica (Cohen and Carlton 1995), clam reproductive activity and benthic, macroinvertebrate community structure are reported for a mudflat one kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay. This report includes data collected for the period January to December 2005, and extends a critical long-term biogeochemical record dating back to 1974. These data serve as the basis for the City of Palo Altos Near-Field Receiving Water Monitoring Program, initiated in 1994.

Metal concentrations in both sediments and clam tissue during 2005 were consistent with results observed since 1990. Copper and zinc concentrations in sediment and bivalve tissue displayed a continued decrease over the last decade. In 2005, Cu concentrations were at or below the effects range-low (ERL) concentration (34 g/g) for the entire year, the first time this has been observed. Also, zinc concentrations never exceeded the ERL (150 g/g). Yearly average concentrations of copper, zinc and silver in Macoma petalum for 2005 were some of the lowest recorded since monitoring for metals began in 1975. The concentrations of mercury and selenium in sediments, during April and January 2004, respectively, were the highest values observed for these elements during this study. Later in 2005, concentrations decreased to historic levels. The increase in mercury and selenium in 2004 was not a permanent trend and concentrations of these elements in sediments and clams at Palo Alto remain similar to concentrations observed elsewhere in the San Francisco Bay.

Analyses of the benthic-community structure of a mudflat in South San Francisco Bay over a 31-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinal clam Macoma petalum from the same area. Analysis of the reproductive activity of M. petalum shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable with almost all animals initiating reproduction in the fall and spawning the following spring of most years. The community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that suggests a more stable community that is subjected to less stress. In addition, two of the opportunistic species (Ampelisca abdita and Streblospio benedicti) that brood their young and live on the surface of the sediment in tubes have shown a continual decline in dominance coincident with the decline in metals. Heteromastus filiformis, a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying their eggs on or in the sediment has shown a concurrent increase in dominance. These changes in species dominance reflect a change in the community from one dominated by surface dwelling, brooding species to one with species with varying life history characteristics. For the first time since its invasion in 1986, the non-indigenous filter-feeding bivalve Corbula (Potamocorbula) amurensis has shown up in small but persistent numbers in the benthic community.

Table of Contents



Environmental Monitoring




Study Site


Sampling Frequency

Measurements of Metal Exposure

Biological Response

Results and Discussion



Clam Tissue

Reproduction of Macoma petalum

Benthic Community


Long-term Observations


Value of Long-Term Monitoring




Appendix A

Appendix B

Appendix C

Appendix D

Appendix E

Appendix F

Appendix G

Appendix H

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