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Francis Parcheso

Publications and source records attributed to Francis Parcheso.

At least 19 recordsLinked to original sources
USGS2015

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: 2014

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica ), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer (km) south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in South San Francisco Bay, Calif. This report includes the data collected by U.S. Geological Survey (USGS) scientists for the period January 2014 to December 2014. These append to long-term datasets extending back to 1974, and serve as the basis for the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. Following significant reductions in the late 1980s, silver (Ag) and copper (Cu) concentrations in sediment and M. petalum appear to have stabilized. Data for other metals, including chromium (Cr), mercury (Hg), nickel (Ni), selenium (Se), and zinc (Zn), have been collected since 1994. Over this period, concentrations of these elements have remained relatively constant, aside from seasonal variation that is common to all elements. In 2014, concentrations of Ag and Cu in M. petalum varied seasonally in response to a combination of site-specific metal exposures and annual growth and reproduction, as reported previously. Seasonal patterns for other elements, including Cr, Ni, Zn, Hg, and Se, were generally similar in timing and magnitude as those for Ag and Cu. In M. petalum , all observed elements showed annual maxima in January–February and minima in April, except for Zn, which was lowest in December. In sediments, annual maxima also occurred in January–February, and minima were measured in June and September. In 2014, metal concentrations in both sediments and clam tissue were among the lowest on record. This record suggests that regional-scale factors now largely control sedimentary and bioavailable concentrations of Ag and Cu, as well as other elements of regulatory interest, at the Palo Alto site. Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 40-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum , from the same area. Analysis of 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 (2014), with almost all animals initiating reproduction in the fall and spawning the following spring. The entire infaunal community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that indicates a more stable community that is subjected to fewer stressors. 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; both species had short-lived rebounds in abundance in 2008, 2009, and 2010. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly in 2011–2012 and returned to pre-2011 numbers in 2014. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for deep-dwelling animals like Macoma petalum . However, within two months of this event animals returned to the mudflat. The resilience of the community suggested that the disturbance was not due to a persistent toxin or to anoxia. The reproductive mode of most species present in 2014 is reflective of species that were available either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2014 benthic community data, which showed that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of species that consume the sediment, or filter feed, have pelagic larvae that must survive landing on the sediment, and those that brood their young. USGS scientists view the 2008 disturbance event as a response by the infaunal community to an episodic natural stressor (possibly sediment accretion or a pulse of freshwater), in contrast to the long-term recovery from metal contamination. We will compare this recovery to the long-term recovery observed after the 1970’s when the decline in sediment pollutants was the dominating factor.

California↗
USGS2014

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: 2013

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica ), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in South San Francisco Bay, Calif. This report includes the data collected by U.S. Geological Survey (USGS) scientists for the period January 2013 to December 2013. These data serve as the basis for the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. Following significant reductions in the late 1980s, silver (Ag) and copper (Cu) concentrations in sediment and M. petalum appear to have stabilized. Data for other metals, including chromium (Cr), mercury (Hg), nickel (Ni), selenium (Se), and zinc (Zn), have been collected since 1994. Over this period, concentrations of these elements have remained relatively constant, aside from seasonal variation that is common to all elements. In 2013, concentrations of Ag and Cu in M. petalum varied seasonally in response to a combination of site-specific metal exposures and annual growth and reproduction, as reported previously. Seasonal patterns for other elements, including Cr, Ni, Zn, Hg, and Se, were generally similar in timing and magnitude as those for Ag and Cu. In M. petalum , all observed elements showed annual maxima in January–February and minima in April, except for Zn, which was lowest in December. In sediments, annual maxima also occurred in January–February, and minima were measured in June and September. In 2013, metal concentrations in both sediments and clam tissue were among the lowest concentrations on record. This record suggests that regional-scale factors now largely control sedimentary and bioavailable concentrations of Ag and Cu, as well as other elements of regulatory interest, at the Palo Alto site. Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 40-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum , from the same area. Analysis of the M. petalum community shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable (2013), with almost all animals initiating reproduction in the fall and spawning the following spring. 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 indicates a more stable community that is subjected to fewer stressors. 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; both species had short-lived rebounds in abundance in 2008, 2009, and 2010. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly in 2011–2012 and returned to pre-2011 numbers in 2013. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for those deep-dwelling animals like Macoma petalum . Animals immediately returned to the mudflat in 2008, which was the first indication that the disturbance was not due to a persistent toxin or to anoxia. The reproductive mode of most species present in 2013 is reflective of the species that were available either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2013 benthic community data, which show that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of animals that consume the sediment, filter feed, have pelagic larvae that must survive landing on the sediment, and brood their young. USGS scientists continue to observe the community’s response to the 2008 defaunation event because it allows them to examine the response of the community to a natural disturbance (possible causes include sediment accretion or freshwater inundation) and compare this recovery to the long-term recovery observed in the 1970s when the decline in sediment pollutants was the dominating factor.

California↗
USGS2013

Internal nutrient sources and nutrient distributions in Alviso Pond A3W, California

Within the Alviso Salt Pond complex, California, currently undergoing avian-habitat restoration, pore-water profilers (U.S. Patent 8,051,727 B1) were deployed in triplicate at two contrasting sites in Pond A3W (“Inlet”, near the inflow, and “Deep”, near the middle of the pond; figs. 1 and 2; table 1, note that tables in this report are provided online only as a .xlsx workbook at http://pubs.usgs.gov/of/2013/1128/). Deployments were conducted in 2010 and 2012 during the summer algal-growth season. Specifically, three deployments, each about 7 weeks apart, were undertaken each summer. This study provides the first measurements of the diffusive flux of nutrients across the interface between the pond bed and water column (that is, benthic nutrient flux). These nutrient fluxes are crucial to pond restoration efforts because they typically represent a major (if not the greatest) source of nutrients to the water column in both ponds and other lentic systems. For soluble reactive phosphorus (SRP, the most biologically available form in solution), benthic flux was positive both years (that is, out of the sediment into the water column; table 2), with the exception of the August 2010 deployment, which exhibited nearly negligible but negative flux. Overall, the average SRP flux was significantly greater at Deep (23.9 ± 8.6 micromoles per square meter per hour (µmol-m -2 -h -1 ); all errors shown reflect the 95-percent confidence interval) than Inlet (12.6 ± 4.9 µmol-m -2 -h -1 ). There was much greater temporal variability in SRP flux in the pond than reported for the lower estuary (Topping and others, 2001). For dissolved ammonia, benthic flux was consistently positive on all six sampling trips, and similar to SRP, the fluxes at Deep (258 ± 49 µmol-m -2 -h -1 ) were consistently greater than those at Inlet (28 ± 11 µmol-m -2 -h -1 ). Dissolved ammonia fluxes reported for South San Francisco Bay by Topping and others (2001) fall in between these values. Once again, greater variability for benthic fluxes determined in the pond was observed relative to adjacent South San Francisco Bay. With the near absence of any measurable concentration gradient, dissolved-nitrate fluxes were consistently negligible in the pond. Silica fluxes are often used to represent sediment diagenetic processes that biogeochemically cycle silica (an important algal macronutrient) between biogenic and inorganic phases (Fanning and Pilson, 1974; Emerson and others, 1984). For South San Francisco Bay, those values are consistently positive from core-incubation experiments. In Pond A3W, dissolved-silica fluxes averaged 49 ± 25 µmol-m -2 -h -1 at Inlet and were much higher at Deep (482 ± 370 µmol-m -2 -h -1 ), similar to the spatially variability observed for SRP and dissolved ammonia. An elevated silica flux can stimulate diatom production and subsequent eutrophication effects. Variability in these silica fluxes is consistent with season patterns in pond primary productivity. On the basis of comparisons of dissolved-oxygen flux measurements by profilers and core incubations, it appears that diffusive flux estimates for the sediment in this pond, as one might expected in such benthically productive environments, result in a significant underestimation of true sediment oxygen demand. Therefore, a core incubation experiment was conducted to better quantify the demand. To complement these benthic-flux studies, a diurnal study of nutrient advective flux into and out of the pond was measured during neap and spring tides to provide comparative estimates for allochthonous solute transport (Garret, 2012). Using the two different tides as the probable upper and lower boundaries, we can estimate a range of probable values throughout the year. After converting this advective flux into kg/yr, we can compare it directly to benthic flux estimates for the pond extrapolated over the 2.27 square kilometer (km 2 ) pond surface. Benthic flux of nitrogen species, averaged over all sites and dates, was about 80,000 kilograms per year (kg/yr), well above the adjective flux range of -50 to 1,500 kg/yr. By contrast, the average benthic flux of orthophosphate was about 12,000 kg/yr, well below the advective flux range of 21,500 to 30,000 kg/yr. Initial benthic flux estimates were also made for trace metals, including copper, nickel, iron, and manganese. These analyses indicated that the two sites, Inlet and Deep, have different pore-water profiles, with Inlet exhibiting much higher benthic flux estimates for nickel, iron, and manganese. These initial benthic-flux values reported for macronutrients are particularly impressive in magnitude when one considers that diffusive flux of dissolved solutes based on pore-water profiles provides a conservative determination that may be enhanced by other biogeochemical processes. These enhancement processes (Boudreau and Jorgensen, 2001) include bioturbation, bioirrigation, wind resuspension, and potential groundwater inflows, some of which are captured in core-incubation experiments (Kuwabara and others, 2009). Hence, the values reported herein represent lower bounds to indicate the potential importance of such internal solute sources. The elevated diffusive fluxes for nutrients in the pond relative to the adjacent estuary indicate that vertical nutrient transport between the pond bed and water column is consistently an important (and at times the most important) source of nutrients that stimulate phytoplankton growth in the water column. One might therefore reasonably hypothesize that this benthic transport of biologically reactive solutes (both nutrients and toxicants) represents the most important step at the base of the food web for trophic transfer.

California↗
USGS2013

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, 2012

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in South San Francisco Bay, Calif. This report includes the data collected by U.S. Geological Survey (USGS) scientists for the period January to December 2012. These data serve as the basis for the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. Following significant reductions in the late 1980s, silver (Ag) and copper (Cu) concentrations in sediment and in M. petalum appear to have stabilized. Data for other metals, including chromium (Cr), mercury (Hg), nickel (Ni), selenium (Se), and zinc (Zn), have been collected since 1994. Over this period, concentrations of these elements have remained relatively constant, aside from seasonal variation that is common to all elements. In 2012, concentrations of Ag and Cu in M. petalum varied seasonally in response to a combination of site-specific metal exposures and annual growth and reproduction, as reported for previous time periods. Seasonal patterns for other elements, including Cr, Ni, Zn, Hg, and Se were generally similar in timing and magnitude as those for Ag and Cu. In 2012, metal concentrations in both sediments and clam tissue were among the lowest concentrations on record. This record suggests that regional-scale factors now largely control sedimentary and bioavailable concentrations of Ag and Cu, as well as other elements of regulatory interest, at the Palo Alto site. Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 39-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum, from the same area. Analysis of the M. petalum community shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable (2012), with almost all animals initiating reproduction in the fall and spawning the following spring. 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 indicates a more stable community that is subjected to fewer stressors. 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; both species had short-lived rebounds in abundance in 2008, 2009, and 2010. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly in 2011–2012. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for those deep-dwelling animals like Macoma petalum. Animals immediately returned to the mudflat in 2008, which was the first indication that the disturbance was not due to a persistent toxin or to anoxia. The reproductive mode of most species present in 2012 is reflective of the species that were available either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2012 benthic community data, which show that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of animals that consume the sediment, filter feed, have pelagic larvae that must survive landing on the sediment, and brood their young. USGS scientists continue to observe the community’s response to the 2008 defaunation event because it allows them to examine the response of the community to a natural disturbance (possible causes include sediment accretion or freshwater inundation) and compare this recovery to the long-term recovery observed in the 1970s when the decline in sediment pollutants was the dominating factor.

California↗
USGS2012

Time scales of change in chemical and biological parameters after engineered levee breaches adjacent to Upper Klamath and Agency Lakes, Oregon

Eight sampling trips were coordinated after engineered levee breaches hydrologically reconnected both Upper Klamath Lake and Agency Lake, Oregon, to adjacent wetlands. The reconnection, by a series of explosive blasts, was coordinated by The Nature Conservancy to reclaim wetlands that had for approximately seven decades been leveed for crop production. Sets of nonmetallic porewater profilers (U.S. Patent 8,051,727 B1; November 8, 2011; http://www.uspto.gov/web/patents/patog/ week45/OG/html/1372-2/US08051727-20111108.html.) were deployed during these trips in November 2007, June 2008, May 2009, July 2009, May 2010, August 2010, June 2011, and July 2011 (table 1). Deployments temporally spanned the annual cyanophyte bloom of Aphanizomenon flos-aquae and spatially involved three lake and four wetland sites. Spatial and temporal variation in solute benthic flux was determined by the field team, using the profilers, over an approximately 4-year period beginning 3 days after the levee breaches. The highest flux to the water column of dissolved organic carbon (DOC) was detected in the newly flooded wetland, contrasting negative or insignificant DOC fluxes at adjacent lake sites. Over the multiyear study, DOC benthic fluxes dissipated in the reconnected wetlands, converging to values similar to those for established wetlands and to the adjacent lake (table 2). In contrast to DOC, benthic sources of soluble reactive phosphorus, ammonium, dissolved iron and manganese from within the reconnected wetlands were consistently elevated (that is, significant in magnitude relative to riverine and established-wetland sources) indicating a multi-year time scale for certain chemical changes after the levee breaches (table 2). Colonization of the reconnected wetlands by aquatic benthic invertebrates during the study trended toward the assemblages in established wetlands, providing further evidence of a multiyear transition of this area to permanent aquatic habitat (table 3). Both the lake and wetland benthic environments substantively contribute to macro- and micronutrients in the water column. Wetland areas undergoing restoration, and those being used for water storage, function very differently relatively to the established wetland within the Upper Klamath Lake National Wildlife Refuge, adjacent Upper Klamath Lake. Developing long-term management strategies for water quality in the Upper Klamath Basin requires recognition of the multi-year time scales associated with restoring wetlands that provide natural, seasonal ecosystem function and services.

Oregon↗
USGS2012

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: 2011

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in South San Francisco Bay, Calif. This report includes the data collected by U.S. Geological Survey (USGS) scientists for the period January 2011 to December 2011. These data serve as the basis for the City of Palo Alto's Near-Field Receiving Water Monitoring Program, initiated in 1994. Following significant reductions in the late 1980s, silver (Ag) and copper (Cu) concentrations in sediment and M. petalum appear to have stabilized. Data for other metals, including chromium, mercury, nickel, selenium, and zinc, have been collected since 1994. Over this period, concentrations of these elements have remained relatively constant, aside from seasonal variation that is common to all elements. In 2011, concentrations of Ag and Cu in M. petalum varied seasonally in response to a combination of site-specific metal exposures and annual growth and reproduction, as reported previously. Seasonal patterns for other elements, including Cr, Hg, Ni, Se, and Zn, were generally similar in timing and magnitude as those for Ag and Cu. In 2011, metal concentrations in both sediments and clam tissue were among the lowest concentrations on record. This record suggests that regional-scale factors now largely control sedimentary and bioavailable concentrations of Ag and Cu, as well as other elements of regulatory interest, at the Palo Alto site. Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 38-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum, from the same area. Analysis of the M. petalum community shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable (2011), with almost all animals initiating reproduction in the fall and spawning the following spring. 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 indicates a more stable community that is subjected to fewer stressors. 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; both species had short-lived rebounds in abundance in 2008, 2009, and 2010. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly in 2011. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for those deep-dwelling animals like Macoma petalum. Animals immediately returned to the mudflat in 2008, which was the first indication that the disturbance was not due to a persistent toxin or to anoxia. The reproductive mode of most species present in 2011 is reflective of the species that were available either as pelagic larvae or as mobile adults. Although egg layers were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2011 benthic community data, which show that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of animals that consume the sediment, filter feed, have pelagic larvae that must survive landing on the sediment, and brood their young. USGS scientists continue to observe the community's response to the 2008 defaunation event because it allows them to examine the response of the community to a natural disturbance (possible causes include sediment accretion or freshwater inundation) and compare this recovery to the long-term recovery observed in the 1970s when the decline in sediment pollutants was the dominating factor.

California↗
USGS2011

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: 2010

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica ), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in South San Francisco Bay, Calif. This report includes the data collected for the period January 2010 to December 2010 and extends a critical long-term biogeochemical record that dates back to 1974. These data serve as the basis for the City of Palo Alto’s Near-Field Receiving Water Monitoring Program initiated in 1994. In 2010, metal concentrations in both sediments and clam tissue were among the lowest concentrations on record and consistent with results observed since 1991. Following significant reductions in the late 1980s, silver (Ag) and copper (Cu) concentrations appear to have stabilized. Annual mean concentrations have fluctuated modestly (2–4 fold) in a nondirectional manner. Data for other metals, including chromium, mercury, nickel, selenium, vanadium, and zinc, have been collected since 1994. Over this period, concentrations of these elements, which likely reflect regional inputs and systemwide processes, have remained relatively constant, aside from typical seasonal variation that is common to all elements. Within years, the winter months (January–March) generally exhibit maximum concentrations, with a decline to annual minima in spring through fall. Concentrations of chromium (Cr) and vanadium (V) in sediments have shown an upward trend since 2005. Chromium concentrations are approaching the record maximum levels observed in 2003, and concentrations of V in sediments in 2010 were the highest annual average concentrations on record. Mercury (Hg) concentrations in sediments and M. petalum in 2010 were comparable to concentrations observed in 2009 and were generally consistent with data from previous years. Selenium (Se) concentrations in sediment varied among years and showed no sustained temporal trend. During 2009–2010, sedimentary Se concentrations declined from the record high observed in 2008 to concentrations that were among the lowest on record. Selenium in M. petalum was slightly higher in 2010 than in 2009. Overall, Cu and Ag concentrations in sediments and soft tissues of the clam, M. petalum , remained representative of the concentrations observed since 1991 following significant reductions in the discharge of these elements from the PARWQCP. This indicates that, as with other elements of regulatory interest, regional-scale factors now largely affect sedimentary and bioavailable concentrations of Ag and Cu. Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 37-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum , from the same area. Analysis of the M. petalum community shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable (2010), 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 indicates a more stable community that is subjected to fewer stressors. 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; both species had short-lived rebounds in abundance in 2008, 2009, and 2010. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in last several years prior to 2008, showed a stable population. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for those deep-dwelling animals like Macoma petalum . Animals immediately returned to the mudflat in 2008, which was the first indication that the disturbance was not due to a persistent toxin or to anoxia. The use of functional ecology was highlighted in the 2010 benthic community data, which show that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of animals that consume the sediment, filter feed, have pelagic larvae that must survive landing on the sediment, and brood their young. USGS scientists continue to observe the community’s response to the defaunation event because it allows them to examine the response of the community to a natural disturbance (possible causes include sediment accretion or freshwater inundation) and compare this recovery to the long-term recovery observed in the 1970s when the decline in sediment pollutants was the dominating factor.

California↗
USGS2009

Benthic oxygen demand in three former salt ponds adjacent to south San Francisco Bay, California

Sampling trips were coordinated in the second half of 2008 to examine the interstitial water in the sediment and the overlying bottom waters of three shallow (average depth <1 meter) ponds adjacent to the southern reach of San Francisco Bay (herein referred to as South Bay), which were previously used in commercial salt production. In recent years, the ponds were modified for wetland restoration and management as part of the South Bay Salt Pond Restoration Project. A pore-water profiler, modified for dissolved-oxygen sampling, was used to obtain the first centimeter-scale estimates of the vertical concentration gradients for diffusive-flux determinations. This study, a collaboration between scientists from two disciplines within the U.S. Geological Survey (Water Resources and Biological Resources), provides information necessary for developing and refining pond-management strategies and supports efforts to monitor changes in fish and wildlife assemblages associated with the habitat-restoration program. Between August 27 and September 30, 2008, pore-water profilers were successfully deployed in the South Bay salt ponds A16, A14, and A3W (fig. 1; fig. 2; table1), measuring the concentration gradient of dissolved oxygen near the sediment-water interface. In each pond, profilers were deployed in triplicate at two sites: a shallow site (< 1 meter) and a deep site (> 2 meters). The water column at all deployment sites was monitored with dataloggers for ancillary water-quality parameters (including dissolved oxygen, salinity, specific conductance, temperature, and pH) to facilitate the interpretation of benthic-flux results. Calculated diffusive benthic flux of dissolved (0.2-micron filtered) oxygen was consistently negative (that is, drawn from the water column into the sediment) and ranged between -0.5 x 10-6 and -37 x 10-6 micromoles per square centimeter per second (site averages depicted in table 2). Assuming pond areas of 1.0, 1.4, and 2.3 square kilometers for ponds A16, A14, and A3W, respectively, this converts to an oxygen mass flux into the ponds' sediment ranging from -1 to -72 kilograms per day. Diffusive oxygen flux into the benthos (listed as negative) was lowest in pond A14 (-0.5 x 10-6 to -1.8 x 10-6 micromoles per square centimeter per second) compared with diffusive flux estimates for ponds A16 and A3W (site averages -26 x 10-6 to -35 x 10-6 and -34 x 10-6 to -37 x 10-6 micromoles per square centimeter per second, respectively). These initial diffusive-flux estimates are of the order of magnitude of those measured in the South Bay using core-incubation experiments (Topping and others, 2004), which include bioturbation and bioirrigation effects. Estimates of benthic oxygen demand reported herein, based on molecular diffusion, serve as conservative estimates of benthic flux because solute transport across the sediment-water interface can be enhanced by multidisciplinary processes including bioturbation, bioirrigation, ground-water advection, and wind resuspension (Kuwabara and others, 2009).

California↗
USGS2009

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: 2008

Results reported herein include trace element concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica (Cohen and Carlton, 1995)), clam reproductive activity, and benthic macroinvertebrate community structure for a mudflat one kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in South San Francisco Bay. This report includes data collected for the period January 2008 to December 2008 and extends a critical long-term biogeochemical record dating back to 1974. These data serve as the basis for the City of Palo Alto's Near-Field Receiving Water Monitoring Program, initiated in 1994. In 2008, metal concentrations in both sediments and clam tissue were among the lowest concentrations on record and consistent with results observed since 1991. Following significant reductions in the late 1980's, silver (Ag) and copper (Cu) concentrations appeared to have stabilized. Annual mean concentrations have fluctuated modestly (2–4 fold) in a nondirectional manner. Data for other metals, including chromium, mercury, nickel, selenium, vanadium, and zinc, have been collected since 1994. Over this period, concentrations of these elements, which more likely reflect regional inputs and systemwide processes, have remained relatively constant, aside from typical seasonal variation that is common to all elements. Within years, concentrations generally reach maximum in winter months (January–March) and decline to annual minima in spring through fall. Mercury (Hg) in sediments spiked to the highest observed level in January 2008. However, sedimentary concentrations for the rest of the year and concentrations of Hg in M. petalum for the entire year were consistent with data from previous years. Average selenium (Se) concentrations in sediment were the highest on record, but there is no evidence, yet, to suggest a temporal trend of increasing sedimentary Se. Selenium in M. petalum was not elevated relative to past years. Overall, Cu and Ag concentrations in sediments and soft tissues of the clam, M. petalum , remained representative of the concentrations observed since 1991 following significant reductions in the discharge of these elements from PARWQCP, suggesting that, similar to other elements of regulatory interest, regional scale factors now largely influence sedimentary and bioavailable concentrations of Cu and Ag. Analyses of the benthic-community structure of a mudflat in South San Francisco Bay over a 31-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum , from the same area. Analysis of the reproductive activity of M. petalum shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable, with almost all animals initiating reproduction in the fall and spawning the following spring of most years. The community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that suggests a more stable community that is subjected to less stress. In addition, two of the opportunistic species ( Ampelisca abdita and Streblospio benedicti ) that brood their young and live on the surface of the sediment in tubes, have shown a continual decline in dominance coincident with the decline in metals. Heteromastus filiformis , a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying their eggs on or in the sediment, has shown a concurrent increase in dominance and is now showing signs of population stability. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for those deep dwelling animals like Macoma petalum . Animals immediately returned to the mudflat, which is indicative that the disturbance was not due to a persistent toxin or due to anoxia. This event allows us to examine the response of the mudflat benthic community to a natural disturbance (possible causes include sediment accretion or freshwater inundation) and compare this recovery to the longer term recovery we observed in the 1970s.

California↗
USGS2009

Benthic flux of nutrients and trace metals in the northern component of San Francisco Bay, California

Two sets of sampling trips were coordinated in late summer 2008 (weeks of July 8 and August 6) to sample the interstitial and overlying bottom waters at 10 shallow locations (9 sites <3 meters in depth) within the northern component of the San Francisco Bay/Delta (herein referred to as North Bay). The work was performed to better understand sources of biologically reactive solutes (namely, dissolved macronutrients and trace metals) that may affect the base of the food web in this part of the estuary. A nonmetallic pore-water profiler was used to obtain the first centimeter-scale estimates of the vertical solute-concentration gradients for diffusive-flux determinations. This study, performed in collaboration with scientists from San Francisco State University?s Romberg Tiburon Center for Environmental Studies, provides information to assist in developing and refining management strategies for the Bay/Delta system and supports efforts to monitor changes in food-web structure associated with regional habitat modifications directed by the California Bay-Delta Authority. On July 7, 2008, and August 5, 2008, pore-water profilers were successfully deployed at six North Bay sites per trip to measure the concentration gradient of dissolved macronutrients and trace metals near the sediment-water interface. Only two of the sites (433 and SSB009 within Honker Bay) were sampled in both series of profiler deployments. At each sampling site, profilers were deployed in triplicate, while discrete samples and dataloggers were used to collect ancillary data from both the water column and benthos to help interpret diffusive-flux measurements. Benthic flux of dissolved (0.2-micron filtered) inorganic phosphate (that is, soluble reactive phosphorus (SRP)) ranged from negligible levels (-0.003?0.005 millimole per square meter per day (mmole m-2d-1) at Site 4.1 outside Honker Bay) to 0.060?0.006 mmole m-2d-1 near the northern coast of Brown?s Island. Except for the elevated flux at Browns Island, the benthic flux of soluble reactive phosphorus (SRP) was consistently: (1) lower than previously reported for South Bay sites, (2) an order of magnitude lower than oligotrophic Coeur d?Alene Lake, (3) two orders of magnitude lower than determined for eutrophic Upper Klamath Lake, and (4) an order of magnitude or more lower than the estimated summer riverine inputs for SRP (900 to 1,300 kilograms of phosphorous per day (kg-P d-1)). In contrast to fluxes reported for the South Bay, nitrate fluxes were consistently negative (that is, drawn from the water column into the sediment), except for one site with statistically insignificant nitrate fluxes (Site 409 within Suisun Bay). The most negative nitrate flux (-7.3?0.1 mmole m-2d-1) was observed within Grizzly Bay (Site 416). Observed nitrate fluxes bracketed the estimated summer fluvial flux of nitrate (3,500 to 5,000 kg-N d-1). With the exception of the two Grizzly Bay sites (416 and 417), the consistently positive benthic flux of ammonia generally counteracted the negative flux of nitrate to yield a net balance of dissolved inorganic nitrogen. Ammonia benthic fluxes extrapolated for Suisun Bay ranged from 320 kg-N d-1 (Site SSB009 near the entrance to Honker Bay) to 1,900 kg-N d-1 (Montezuma Island). These values represent a significant ammonia source to the water column relative to summer riverine inputs (approximately 400 to 600 kg-N d-1). Dissolved silica also displayed a consistently positive benthic flux, except for Site 409 within Suisun Bay, which showed insignificant fluxes (also insignificant for nitrate and SRP). As with the nitrate fluxes, Grizzly Bay and Browns Island sites yielded the highest dissolved silica fluxes (1.3?1.2 to 2.5?0.6 mmole m-2d-1, respectively). These initial diffusive-flux estimates are greater than those measured in the South Bay using core-incubation experiments, which include bioturbation and bioirrigation effects, but they are nevertheless probably one to t

Open-File Report↗
USGS2008

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: 2007

Results reported herein include trace element concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica (Cohen and Carlton 1995)), clam reproductive activity, and benthic macroinvertebrate community structure for a mudflat one kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay. This report includes data collected for the period January 2007 to December 2007, and extends a critical long-term biogeochemical record dating back to 1974. These data serve as the basis for the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. Metal concentrations in both sediments and clam tissue during 2007 remained consistent with results observed since 1990. Most notably, copper and silver concentrations in sediment and clam tissue are elevated for the second consecutive year, but the values remain well within the range of past findings. Other metals such as chromium, nickel, vanadium, and zinc remained relatively constant throughout the year except for maximum values that generally occur in winter months (January-March). Mercury levels in sediment and clam tissue were some of the lowest seen on record. Last year’s elevated selenium levels appear to be transient, and selenium concentrations have returned to background levels. Overall, metal concentrations in sediments and tissue remain within past findings. Analyses of the benthic-community structure of a mudflat in South San Francisco Bay over a 31-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum , from the same area. Analysis of the reproductive activity of M. petalum shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable, with almost all animals initiating reproduction in the fall and spawning the following spring of most years. The community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that suggests a more stable community that is subjected to less stress. In addition, two of the opportunistic species ( Ampelisca abdita and Streblospio benedicti ) that brood their young and live on the surface of the sediment in tubes, have shown a continual decline in dominance coincident with the decline in metals. Heteromastus filiformis , a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying their eggs on or in the sediment, has shown a concurrent increase in dominance and is now showing signs of population stability. 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.

California↗
USGS2007

Near-field receiving water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California--2006

Results reported herein include trace element concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica (Cohen and Carlton 1995)), clam reproductive activity, and benthic macroinvertebrate community structure for a mudflat one kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay. This report includes data collected for the period January 2006 to December 2006, and extends a critical long-term biogeochemical record dating back to 1974. These data serve as the basis for the City of Palo Alto's Near-Field Receiving Water Monitoring Program, initiated in 1994. Metal concentrations in both sediments and clam tissue during 2006 were consistent with results observed since 1990. Most notably, copper and silver concentrations in sediment and clam tissue increased in the last year but the values remain well within range of past data. Other metals such as chromium, nickel, vanadium, and zinc remained relatively constant throughout the year except for maximum values generally occurring in winter months (January-March). Mercury levels in sediment and clam tissue were some of the lowest seen on record. Conversely, selenium concentrations reached a maximum level but soon returned to baseline levels. In all, metal concentrations in sediments and tissue remain within past findings. There are no obvious directional trends (increasing or decreasing). Analyses of the benthic-community structure of a mudflat in South San Francisco Bay over a 31-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam M. petalum from the same area. Analysis of the reproductive activity of M. petalum shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable, with almost all animals initiating reproduction in the fall and spawning the following spring of most years. The community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that suggests a more stable community that is subjected to less stress. In addition, two of the opportunistic species (Ampelisca abdita and Streblospio benedicti) that brood their young and live on the surface of the sediment in tubes, have shown a continual decline in dominance coincident with the decline in metals. Heteromastus filiformis, a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles 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 clam Corbula (Potamocorbula) amurensis has shown up in small, but persistent, numbers in the benthic community.

California↗
USGS2007

Quantifying the benthic source of nutrients to the water column of Upper Klamath Lake, Oregon

Executive Summary Five sampling trips were coordinated in April, May and August 2006, and May and July 2007 to sample the water column and benthos of Upper Klamath Lake, OR (Fig. 1; Table 1), before, during and after the annual cyanophyte bloom of Aphanizomenon flos-aquae (AFA). A pore-water profiler was designed and fabricated to obtain the first high-resolution (centimeter-scale) estimates of the vertical concentration gradients for diffusive-flux determinations. Estimates based on molecular diffusion may underestimate benthic flux because solute transport across the sediment-water interface can be enhanced by processes including bioturbation, bioirrigation and ground-water advection. Water-column and benthic samples were also collected to help interpret spatial and temporal trends in diffusive-flux estimates. Data from these samples complement geochemical analyses of bottom-sediments taken from Upper Klamath Lake (UKL) in 2005. This ongoing study provides information necessary for developing process-interdependent solute-transport models for the watershed (that is, models integrating physical, geochemical and biological processes), and supports efforts to evaluate remediation or load-allocation strategies. To augment studies funded by the U.S. Bureau of Reclamation (USBR), the Department of Interior supported an additional full deployment of pore-water profilers in July 2007, during the summer AFA bloom. Results from this recent field trip are not fully completed. Data not presented herein will be included in a subsequent publication, scheduled for March 2009.

Oregon↗
USGS2006

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

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 Alto’s 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 µg/g) for the entire year, the first time this has been observed. Also, zinc concentrations never exceeded the ERL (150 µg/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 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.

California↗
USGS2004

Near-field receiving water monitoring of a benthic community near the Palo Alto Water Quality Control Plant in south San Francisco Bay: February 1974 through December 2003

Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 29-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 balthica from the same area. 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 could be indicative of 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. Analysis of the reproductive activity of Macoma balthica shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissue of this organism. Reproductive activity is presently stable with almost all animals reproducing during the two reproductive seasons (spring and fall) of most years. These findings are consistent with findings previously reported for the 1974 through 2002 period.

California↗
USGS2003

Near-field receiving water monitoring of a benthic community near the Palo Alto Water Quality Control Plant in South San Francisco Bay: February 1974 through December 2002

Analyses of the benthic community structure over a 28-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 balthica from the same area. 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 could be indicative of 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. Analysis of the reproductive activity of Macoma balthica shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissue of this organism. Reproductive activity is presently stable with almost all animals reproducing during the two reproductive seasons (spring and fall) of most years. These findings are consistent with findings previously reported for the 1974 through 2000 period.

California↗