Geology topics

Francis Parchaso

Publications and source records attributed to Francis Parchaso.

At least 19 recordsLinked to original sources

USGS2026

Biophysical controls on sediment erodibility in shallow estuarine embayments

The erodibility of cohesive sediment is known to vary both spatially and temporally but the factors governing its variation are not well understood. We conducted a field investigation of the influence of hydrodynamic forcing, sediment properties, and benthic infauna on erodibility in the muddy shallows of San Pablo and Grizzly Bays in northern San Francisco Bay in summer 2019 and winter 2020. An erosion rate parameter M c was determined from regressions between near-bed vertical turbulent sediment flux, as a proxy for erosion, and bed shear stress due to currents. During each 2-month study period, we measured benthic infauna abundance and dry bulk density, particle size distribution, percent organic carbon, chlorophyll a , pheophytin a , and carbohydrates carbon concentrations of surficial bed sediments five or six times. M c increased with bed shear stress due to waves in both embayments. In San Pablo Bay, erodibility was approximately 50% lower during the winter than the summer deployment, whereas in Grizzly Bay, there was no significant difference. The factor most strongly related to the decrease in M c in San Pablo Bay was increased abundance of the amphipod Ampelisca abdita . The observed reduction in erodibility may occur in many muddy estuaries because A. abdita is broadly distributed in the coastal waters of North America. Erodibility was also directly related to biomass of the invasive clam Potamocorbula amurensis . Erodibility did not depend on dry bulk density: bulk density did not vary seasonally in San Pablo Bay and was lower in winter than summer in Grizzly Bay.

California↗

USGS2025

Disentangling geomorphic equifinality in sediment and hydrologic connectivity through the analyses of landscape drivers of hysteresis

Sources, transport mechanisms and pathways of fine sediment in river systems are dependent on a multitude of climatic, geomorphic and anthropogenic factors, resulting in geomorphic equifinality, in which it is difficult to parse how different landscape processes affect sediment transport across different spatiotemporal scales. The objectives of this study are to 1) provide a conceptual model to consider how differing spatial distributions and hydrologic timing of sediment sources, both upland and in-channel, can result in equifinal sediment transport outcomes, and 2) utilize analytical methods with widely available environmental datasets to infer sediment processes from stream gaging data. Hysteretic patterns of observed storm events were classified based on their direction and timing of peak sediment concentration, relative to streamflow, using records from 35 U.S. Geological Survey stream gages in the period between 2007 and 2023 within two different physiographic regions: the Mid-Atlantic Delaware River Basin (DRB) and the Midwestern Illinois River Basin (IRB). The DRB contains mixed forest, urban, suburban and agricultural watersheds over diverse topography, and the IRB is primarily an intensively managed agricultural watershed on flat terrain. We use principal component analysis and linear discriminant analysis to infer regional hydrologic relations with turbidity dynamics, and to identify the primary hydrologic and land surface characteristics most effective at distinguishing between hysteretic classes in each region. These analyses reveal underlying regional relations in storm event hydrodynamics and landscape characteristics that contribute to varying patterns in sediment dynamics. Incorporating these sediment dynamic relations with spatial distributions and hydrologic timing of sediment sources could help to improve process understanding and predictive capability of fine sediment transport in watersheds.

Delaware, Illinois, Indiana, New Jersey, New York,↗

USGS2024

State of science, gap analysis, and prioritization for southeastern United States water-quality impacts from coastal storms—Fiscal year 2023 program report to the Water Resources Mission Area from the Water Availability Impacts of Extreme Events Program—Hurricanes

Tropical cyclones (coastal storm events that include tropical depressions, tropical storms, and hurricanes) cause landscape-scale disturbances that can lead to impaired water quality and thus reduce water availability for use. Stakeholders and scientists at local and national scales have illustrated a need for understanding these risks to water quality. A regional and comprehensive understanding of the impacts of tropical storms and hurricanes on surface-water and groundwater quality—and thus water availability—is lacking for potentially impacted coastal and inland areas. As the U.S. Geological Survey considers development of tools to predict the extent to which water-quality impacts of hurricanes affect water availability, an assessment of the state of the science of hurricane impacts is needed, including a gap analysis and prioritization of data and science needs. This assessment focuses on the southeastern coastal States.

southeastern United States↗

USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California↗

USGS2023

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—2020

Trace-metal concentrations in sediment and in the clam Limecola petalum (World Register of Marine Species, 2020; formerly reported as Macoma balthica and M. petalum ), 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, California. This report includes the data collected by the U.S. Geological Survey (USGS) for January 2020–December 2020 (Cain and others, 2022). These data append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2020 data within the context of the longer, multidecadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving- Water Monitoring Program, initiated in 1994. Silver and copper contamination substantially decreased at the site in the 1980s following the implementation by PARWQCP of advanced wastewater-treatment and source-control measures. Since the 1990s, concentrations of these elements in surface sediments have continued to decrease, although more slowly. For example, from 1994 to 2020, the minimum annual mean silver concentration—0.20 milligram per kilogram (mg/kg)—was observed in multiple years. In 2020, silver concentrations ranged from 0.18 to 0.28 mg/kg. These concentrations are 2 to 3 times higher than the regional background concentration. Presently (2020), sediment-copper concentrations appear to be near the regional background level. Over the same period (1994–2020), sedimentary iron and zinc exhibited modest decreases. Sedimentary aluminum, chromium, mercury, nickel, and selenium have not exhibited any trend. Since 1994, silver and copper concentrations in L. petalum have varied seasonally, apparently in response to a combination of site-specific metal exposures and cyclic growth and reproduction, as reported previously. Seasonal patterns for other elements, including chromium, mercury, nickel, selenium, and zinc, generally were similar in timing and magnitude as those for silver and copper. Downward trends in the silver and zinc concentrations in L. petalum during 1994–2020 were evident and appeared to be related to the general physiological condition of the clam, indicated by a condition index. Biological effects of elevated silver and copper contamination at the Palo Alto site have been interpreted from data collected during and after the recession of these contaminants. Concentrations of both elements in the soft tissues of L. petalum decreased with sedimentary copper and silver. This pattern was associated with changes in the reproductive activity of L. petalum , as well as the structure of the benthic invertebrate community. Reproductive activity of L. petalum increased as metal concentrations in L. petalum decreased (Hornberger and others, 2000), and presently is stable with almost all animals initiating reproduction in the fall and spawning the following spring. Analyses of the benthic community structure indicate that the infaunal invertebrate community has shifted from one dominated by several opportunistic species when silver and copper exposures were highest to one in which the species abundance is more evenly distributed, a pattern that indicates a more stable community that is subjected to fewer stressors. Importantly, this long-term change is unrelated to other metals and other measured environmental factors, including salinity and sediment composition. 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 decrease in dominance coincident with the decrease in metals. Both species had short-lived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 2020. 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 from 2011 to 2012 and returned to pre-2011 numbers in 2020. The reproductive mode of most species that were present in 2020 was indicative of species that were capable of movement 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 2020 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, those that have pelagic larvae that must survive landing on the sediment, and those that brood their young. The long-term recovery observed after the 1970s can be ascribed to the decrease in sediment pollutants.

California↗

USGS2023

Bivalve effects on the food web supporting delta smelt—A long-term study of bivalve recruitment, biomass, and grazing rate patterns with varying freshwater outflow

Phytoplankton are an important and limiting food source in the Sacramento-San Joaquin Delta and San Francisco Bay in California. Decreasing phytoplankton biomass is one possible factor for the pelagic organism decline and the decline of the protected Hypomesus transpacificus (delta smelt). Bivalves Corbicula fluminea and Potamocorbula amurensis (hereafter C. fluminea and P. amurensis , respectively) have been shown to control phytoplankton biomass throughout San Francisco Bay and the Sacramento-San Joaquin Delta; therefore, their distribution and population dynamics are of great interest. We describe the distribution and dynamics of bivalve biomass using samples from California Department of Water Resources’ (DWR) 2019 benthic monitoring program. As one element of DWR’s and the Bureau of Reclamation’s Environmental Monitoring Program (EMP), the DWR benthic monitoring program examines the effect of water project operations on the estuary as prescribed by a series of Water Rights Decisions mandated by the California State Water Resources Control Board (SWRCB). The biomass and grazing rate values of both bivalves had similar patterns, therefore, comments on biomass distribution can be applied to grazing rate data. Biomass and recruitment values of C. fluminea were too low at station C9 (Old River upstream from Clift on Court Forebay Intake) to describe a temporal pattern. Corbicula fluminea biomass values were consistently high at station D24 (Sacramento River). Station D4L (confluence of San Joaquin and Sacramento Rivers) biomass values were low during the first half of the year and high the rest of the year. Corbicula fluminea biomass values at station P8 (San Joaquin River) were the highest and most consistent on that river. Station D16 (San Joaquin River) and station D28A (central delta) biomass values were near zero with a small peak in May. Potamocorbula amurensis biomass values were near zero at station D4L (confluence of San Joaquin and Sacramento Rivers). Biomass values were strongly seasonal at station D6 (Suisun Bay). Station D41 (San Pablo Bay) had the highest P. amurensis biomass values. Station D7 (Grizzly Bay) and station D41A (San Pablo Bay) had low biomass values in January-June or July and maximum biomass values in August. Corbicula fluminea recruits in the Sacramento River stations peaked twice, from January to June and from September to December. At the San Joaquin River stations, C. fluminea recruitment peaked from May to July or August and from November to December. Peak recruit abundance was higher on the Sacramento River than the San Joaquin River. Potamocorbula amurensis recruitment was more seasonal than C. fluminea , with a high number of recruits followed by periods with no recruits. Station D4L had few recruits except in January. Station D6 had low recruitment from January to February, increased in August, and peaked from November to December. Station D7 had fewer recruits than station D6 but had a similar temporal pattern, although winter recruits continued into April instead of February. Station D41 recruits were sparce and present only from May to July. Station D41A had the most recruits from January to July, and again in September.

California↗

USGS2023

Bivalve effects on the food web supporting delta smelt—A spatially intensive study of bivalve recruitment, biomass, and grazing rate patterns with varying freshwater outflow in 2019

Phytoplankton are an important and limiting food source in the Sacramento-San Joaquin Delta and San Francisco Bay. The decline of phytoplankton biomass is one potential factor in the decline of the protected Hypomesus transpacificus (delta smelt) and other pelagic organisms. The bivalves Corbicula fluminea and Potamocorbula amurensis (hereafter C. fluminea and P. amurensis , respectively) have been shown to control phytoplankton biomass in several locations throughout the San Francisco Bay and the Sacramento-San Joaquin Delta; therefore, knowledge of their distribution and population dynamics are of great interest. Here, we describe the distribution and dynamics of bivalve biomass using samples collected by the California Department of Water Resources (DWR) as part of the benthic monitoring program in 2019. One element of DWR’s and the Bureau of Reclamation’s Environmental Monitoring Program—the Generalized Random Tessellation Stratified (GRTS) program—examines the spatial and temporal extent of C. fluminea and P. amurensis control on phytoplankton. Historically, the GRTS program sampled 175 benthic stations (50 stations that are monitored every year and 125 randomly selected new stations that are changed yearly) throughout the Sacramento-San Joaquin Delta and northern San Francisco Bay (San Pablo and Suisun Bays) during one week in May and October. In 2019, only the 50 annually replicated stations were sampled. Corbicula fluminea and P. amurensis biomass and grazing rates had similar trends; therefore, the conclusions regarding biomass are applied to grazing rate data as well. Corbicula fluminea biomass decreased from May to October, whereas P. amurensis average biomass (reported increased from May (1 g ash-free-dry-tissue mass/square meter (g AFDM/m 2 ) to October (2 g AFDM/m 2 ). Although C. fluminea ’s average biomass was lower in October (10 gAFDM/m 2 ) than in May (20 gAFDM/m 2 ), the highest single biomass value was also observed in October (300 gAFDM/m 2 ). In both May and October, most stations that recorded high C. fluminea biomass values were located in the deep water (≥3 m of depth between the surface of the water and the surface of the substrate on the bottom) and were sampled in either rivers or sloughs. A relation between depth and biomass was not observed for P. amurensis . Both C. fluminea and P. amurensis recruitment (recruits are considered animals ≤2.5mm in length in this study and recruitment is the process of recruits successfully settled to the bottom) increased from May to October. The total number of C. fluminea recruits more than doubled from May to October, whereas P. amurensis total recruitment increased by 8-fold during the same period. Most P. amurensis recruits in May can be attributed to one station, whereas the recruits in October were found at 14 stations. A relation between number of recruits and station depth was not evident for either C. fluminea or P. amurensis .

California↗

USGS2021

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—2019

Trace-metal concentrations in sediment and in the clam Limecola petalum (formerly reported as Macoma balthica and M. petalum ), 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 the U.S. Geological Survey (USGS) for the period January 2019 to December 2019. These data append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2019 data within the context of the longer, multidecadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving-Water Monitoring Program, initiated in 1994. Significant reductions in silver and copper contamination occurred at the site in the 1980s following the implementation by PARWQCP of advanced wastewater treatment and source control measures. Since the 1990s, concentrations of these elements in surface sediments have continued to decrease, although more slowly. Silver appears to have stabilized at concentrations about twice the regional background concentration. Presently, sediment copper concentrations appear to be near the regional background level. Over the same period (1994–2019), sedimentary iron and zinc also exhibited modest declines. Sedimentary aluminum, chromium, mercury, nickel, and selenium have not exhibited any trend. Since 1994, concentrations of silver and copper in L. petalum have varied seasonally, apparently in response to a combination of site-specific metal exposures and cyclic growth and reproduction, as reported previously. Seasonal patterns for other elements, including chromium, mercury, nickel, selenium, and zinc, were generally similar in timing and magnitude as those for silver and copper. The annual growth and reproductive cycle explained a small amount of the variance in annual silver and zinc tissue metal concentrations. However, interannual trends are not apparent for any element. Biological effects of elevated silver and copper contamination at the Palo Alto site have been interpreted from data collected during and after the recession of these contaminants. Concentrations of both elements in the soft tissues of L. petalum declined with sedimentary copper and silver. This pattern was associated with changes in the reproductive activity of L. petalum , as well as the structure of the benthic invertebrate community. Reproductive activity of L. petalum increased as metal concentrations in L. petalum declined and presently is stable with almost all animals initiating reproduction in the fall and spawning the following spring. Analyses of the benthic community structure indicate that the infaunal invertebrate community has shifted from one dominated by several opportunistic species when silver and copper exposures were highest to one in which the species abundance is more evenly distributed, a pattern that indicates a more stable community that is subjected to fewer stressors. Importantly, this long-term change is unrelated to other metals and other measured environmental factors, including salinity and sediment composition. 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 and showed signs of increasing abundance in 2019. 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 2019. 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 L. petalum . However, within two months of this event, animals returned to the mudflat. The resilience of the community suggested that the disturbance was not caused by a persistent toxin or anoxia. The reproductive mode of most species that were present in 2019 was indicative 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 2019 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, those that 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 1970s when the decline in sediment pollutants was the dominating factor.

California↗

USGS2021

Effect of the emergency drought barrier on the distribution, biomass, and grazing rate of the bivalves Corbicula fluminea and Potamocorbula amurensis, False River, California

Executive Summary Benthic samples were collected from the Sacramento–San Joaquin Delta of northern California to examine the effect of the changing hydrologic flow on the bivalves Potamocorbula and Corbicula before, during, and after the False River Barrier (hereafter, barrier) was in operation (May–November 2015). Potamocorbula moved upstream in the Sacramento River as the salinity intruded. Given the lower electrical conductivity of the San Joaquin River, Potamocorbula did not move as far upriver as it did in the Sacramento River. Potamocorbula recruits settled in the Sacramento and False Rivers, whereas Corbicula recruits were mostly found in the San Joaquin River. When the grazing rates for the two bivalves were combined, new populations of Potamocorbula plus existing Corbicula likely reduced the net growth rate of the phytoplankton in and just upstream from the Sacramento and San Joaquin River confluence region when the barrier was in place. Prior to the barrier installation, a very dry period assumably aided the success of Potamocorbula in the confluence region; nonetheless, they also responded to the increasing salinity in the Sacramento River and their population spatially expanded. Potamocorbula’s upriver incursion was stopped owing to the return of freshwater flow due to the removal of the barrier, but the adults of the species were still present at the upstream end of Decker Island in January 2016. Corbicula adults did not seem to respond to the increased salinity caused by the barrier and maintained their biomass at all locations compared to what was recorded before the barrier.

California↗

USGS2021

If you give a clam an estuary: The story of potamocorbula

When you look at San Francisco Bay, what animals do you see? You may see lots of fish swimming around and birds flying above. What you DON’T see is Potamocorbula, a little clam that has had a big impact. Many years ago, ships accidentally brought Potamocorbula into the Bay. Pretty soon, Potamocorbula spread out all over in large numbers! Clams pump water over their gills and eat small particles of food, like phytoplankton, that pass through with the water. Potamocorbula can pump water much faster than other clams that live in the Bay, and they can eat more than their share of phytoplankton. Sometimes Potamocorbula eats phytoplankton faster than phytoplankton can grow! What problems does that cause for other animals, like birds and fish, that also need phytoplankton? Does Potamocorbula’s invasion only have negative impacts? In this article, we dive to the bottom of the Bay to find some answers. Book series publishing the chapter: https://kids.frontiersin.org/collection/13528/where-the-river-meets-the-ocean-stories-from-san-francisco-estuary

California↗

USGS2019

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—2018

California↗

USGS2019

Benthic community dynamics in Coyote Creek and Artesian Slough, southern San Francisco Bay, California, May 2016 to March 2018

The primary objective of this study is to quantify current (2016–18) benthic-community structure and function in the southern San Francisco Bay, and to compare those communities to the communities in the neighboring sloughs. The study area is inclusive of the area south of the Dumbarton Bridge including Coyote Creek and Artesian Slough. The southern San Francisco Bay is a system dependent on phytoplankton as the base to the food web. Despite abundant nutrients, southern San Francisco Bay has had limited phytoplankton production in the last several decades owing to poor light conditions caused by high turbidities, and high grazing losses from the water column by benthic invertebrates and zooplankton. However, the balance of biogeochemical conditions during spring of most years accommodates a short phytoplankton bloom in the southern San Francisco Bay. This balance between available light, nutrients, and grazing has maintained the phytoplankton biomass in the southern San Francisco Bay at low levels relative to other high-nutrient urban estuaries. The role of benthic invertebrates during episodic spring events, as well as in other seasons, remains of great interest to water-quality and biological resource managers.

California↗

USGS2018

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—2017

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 2017 to December 2017. These append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2017 data within the context of the longer, multi-decadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. Significant reductions in silver and copper concentrations in sediment and M. petalum occurred at the site in the 1980s following the implementation by PARWQCP of advanced wastewater treatment and source control measures. Since the 1990s, concentrations of these elements appear to have stabilized at concentrations somewhat above silver (Ag) or near copper (Cu) regional background concentrations. 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 2017, concentrations of silver and copper 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. This record suggests that legacy contamination and regional-scale factors now largely control sedimentary and bioavailable concentrations of silver and copper, 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 (2017), 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 and showed signs of increasing abundance in 2017. 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 2017. 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 M. 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 anoxia. The reproductive mode of most species that were present in 2017 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 2017 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 1970s when the decline in sediment pollutants was the dominating factor.

California↗

USGS2017

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; 2016

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 2014 to December 2016. These append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2016 data within the context of the longer, multi-decadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994. Significant reductions in silver and copper concentrations in sediment and M. petalum occurred at the site in the 1980s following the implementation by PARWQCP of advanced wastewater treatment and source control measures. Since the 1990s, concentrations of these elements appear to have stabilized at concentrations somewhat above (silver) or near (copper) regional background concentrations 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 2016, concentrations of silver and copper 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. This record suggests that legacy contamination and regional-scale factors now largely control sedimentary and bioavailable concentrations of silver and copper, 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 (2016), 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 and showed signs of increasing abundance in 2016. 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 2016. 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 anoxia. The reproductive mode of most species present in 2016 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 2016 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 1970s when the decline in sediment pollutants was the dominating factor.

California↗

USGS2017

Conceptual model for invasive bivalve control on wetland productivity

Tidal wetlands were the historically dominant features of many coastal regions around the world, including the San Francisco Estuary (Callaway et al. 2011; Whipple et al. 2012). These mosaics of varied interconnected habitats (Mitsch and Gosselink 1993) provide a host of ecosystem services, including biodiversity maintenance, fish and wildlife habitat, water quality improvement, flood abatement, and carbon sequestration (Rabenhorst 1995; Costanza et al. 1997; Bottom et al. 2005; Zedler and Kercher 2005; Barbier et al. 2010). They also support human activities and values such as recreation and aesthetic appreciation (Barbier et al. 2010; Milligan and Kraus-Polk 2016). Despite their critical functions, many wetland landscapes have been destroyed or irreparably altered, either incidentally or intentionally, by human activities (Holland et al. 2004; Zedler and Kercher 2005; Callaway et al. 2011; Cloern and Jassby 2012; Whipple et al. 2012; Schile et al. 2014). San Francisco Estuary (SFE) (see Figure 1) tidal wetlands were largely converted to other land uses in the late 1800s and early 1900s, with the extent of loss and new use varying by region. Wetland losses in the North, Central, and South San Francisco bays and Suisun Bay ranged from 70 percent to 93 percent to accommodate agricultural uses, salt production, managed waterfowl habitat, and urban development (Callaway et al. 2011). Landscape transformation within the most inland portion of the SFE, the Sacramento-San Joaquin Delta (Delta), was even more dramatic. Overall, today’s Delta contains 97 percent less freshwater tidal wetland than its historical state and nearly double the open water area (Whipple et al. 2012). The majority of the modern Delta consists of agricultural tracts protected from tidal waters by human-made dikes or levees, which are commonly armored with riprap. The de-watered, rich peat soils of these created islands have supported abundant agricultural production, but have oxidized, compacted, and blown away in the process, causing significant subsidence (Deverel and Leighton 2010). Occasional levee failures turn islands into lakes; a few large shallow lakes remain after accidental levee breaches were not repaired (Whipple et al. 2012).

California↗

USGS2016

Benthic processes affecting contaminant transport in Upper Klamath Lake, Oregon

Executive Summary Multiple sampling trips during calendar years 2013 through 2015 were coordinated to provide measurements of interdependent benthic processes that potentially affect contaminant transport in Upper Klamath Lake (UKL), Oregon. The measurements were motivated by recognition that such internal processes (for example, solute benthic flux, bioturbation and solute efflux by benthic invertebrates, and physical groundwater-surface water interactions) were not integrated into existing management models for UKL. Up until 2013, all of the benthic-flux studies generally had been limited spatially to a number of sites in the northern part of UKL and limited temporally to 2–3 samplings per year. All of the benthic invertebrate studies also had been limited to the northern part of the lake; however, intensive temporal (weekly) studies had previously been completed independent of benthic-flux studies. Therefore, knowledge of both the spatial and temporal variability in benthic flux and benthic invertebrate distributions for the entire lake was lacking. To address these limitations, we completed a lakewide spatial study during 2013 and a coordinated temporal study with weekly sampling of benthic flux and benthic invertebrates during 2014. Field design of the spatially focused study in 2013 involved 21 sites sampled three times as the summer cyanobacterial bloom developed (that is, May 23 , June 13 , and July 3, 2013). Results of the 27-week, temporally focused study of one site in 2014 were summarized and partitioned into three periods (referred to herein as pre-bloom, bloom and post-bloom periods), each period involving 9 weeks of profiler deployments, water column and benthic sampling. Partitioning of the pre-bloom, bloom, and post-bloom periods were based on water-column chlorophyll concentrations and involved the following date intervals, respectively: April 15 through June 10 , June 17 through August 13 , and August 20 through October 16, 2014. To examine dissolved-solute (0.2-micrometer [μm] filtered) benthic flux, sets of nonmetallic pore-water profilers (U.S. Patent 8,051,727 B1) were deployed. In 2013, the deployment of profilers at 21 UKL sites occurred at the beginning of the annual cyanobacterial bloom of Aphanizomenon flos–aquae (AFA), in the middle of the bloom period, and at the peak of the bloom. Coordinated benthic invertebrate collections also were made. Based on results from 2013, weekly deployments of profilers and collection of benthic invertebrate samples from late spring to early autumn were used to estimate temporal trends in solute flux and benthic invertebrate densities. Estimates of nutrient efflux by benthic invertebrates were determined in the spring and autumn from 2011 through 2013 and three times (spring, summer, and autumn) in 2015. This work extends UKL studies that began in 2006 to quantify the importance of benthic solute sources in the lake. In 2015, piezometers and thermistor sets were deployed to quantify potential groundwater exchange with the lake water column. Analysis of the 2013 soluble reactive phosphorus (SRP) benthic flux indicated no effect of location (lake region), habitat, or sampling period, and the average lakewide flux values were consistent with earlier studies that had been confined to the northern region of UKL and adjacent wetlands. The 2014 study therefore focused on estimating temporal trends at a site within Ball Bay. During both 2013 and 2014 field studies, fluxes of macronutrients (soluble reactive phosphorus (SRP) and ammonia) and micronutrients (iron [Fe] and manganese [Mn]) were consistently positive and increased prior to the initial AFA bloom, varied or lagged with water-column chlorophyll during the summer bloom period, then decreased after the cyanobacterial blooms, only to rebound toward pre-bloom conditions in the final weeks of sampling. These four solutes exhibited benthic loads greater than maximum riverine loads estimated during the spring and early summers of 2013 and 2014. However, consistently detectable concentrations for all four solutes provide no evidence that they consistently serve as the limiting nutrient for primary production in the lake. In contrast to the four solutes (SRP, ammonia, Fe, and Mn), benthic fluxes of dissolved arsenic (As) were both negative and positive (that is, the lakebed currently serves as both a source and a sink for dissolved As, depending on season). In a further contrast with SRP, ammonia, dissolved Fe, and Mn, dissolved-As riverine loads to UKL were of similar magnitude to benthic loads. A negative relationship between dissolved-As flux and water-column As over the 2014 temporal study provides a potential advantage for the management of water-quality in contrast to solutes, like SRP or ammonia, with consistently positive flux. The mean total benthic invertebrate density during 2013 was 12,610 individuals per square meter (n=63). Although benthic invertebrate density did not change over the study period, it was higher in littoral habitats than open-lake or trench habitats and higher in the northern region compared to the central or southern regions of UKL. Mean total benthic invertebrate density during 2014 was 19,726 individuals m −2 (n=27). Density during the pre-bloom and bloom periods of April 15 to August 13, 2014 (the first two thirds of the 2014 sampling period), were similar to 2013. However, benthic invertebrate density more than doubled during the latter one-third of the study, that is, the post-bloom period between August 20 to October 16, 2014. Oligochaeta, Chironomidae and Hirudinea represented well over 90 percent of the benthic fauna; Oligochaeta were twice as abundant as Chironomidae or Hirudinea, the latter two of which were similar in density. Benthic invertebrates may enhance dissolved-nutrient (or toxicant) transport across the sediment-water interface by (1) modifying diffusion-layer thicknesses and permeability through bioturbation, (2) enhancing advective flow across the interface through bioirrigation, and (3) excreting or expelling dissolved or particulate solutes directly into the overlying water column (Boudreau and Jorgensen, 2001). We evaluated SRP efflux via excretion for approximately 15 different major taxa in UKL. Once these measures were scaled, it was evident that benthic invertebrates potentially contribute approximately 1.5 times the amount of SRP to the water column of Upper Klamath Lake as diffusive SRP flux alone, measured in profiler deployments. Sets of piezometers and temperature loggers were deployed in UKL to obtain estimates of vertical advective solute flux. The pressure transducer installations, within the piezometers, did not perform as designed, rendering the head gradient data unreliable. However, in terms of future research, this field work did demonstrate the feasibility of collecting vertical gradient data with piezometer deployments. Advective flux estimates herein are based solely on heat-flow modeling based on temperature data from four lake sites, without use of transducer data. Given the magnitudes (both positive or negative) of the heat-transfer fluxes for SRP, relative to diffusive-flux and macroinvertebrate efflux measurements (all positive but spanning the same orders of magnitude), further examination of solute advective flux is recommended as a potential transport process to integrate into existing water-quality (for example, Total Maximum Daily Load [TMDL]) models. As a complement to the biogeochemical focus of this study, initial analyses of suspended-particle (floc) characteristics and settling velocities from the water column were derived near the surface and lakebed at two UKL sites. To better understand changing particle characteristics during the AFA-bloom period, suspended particles were examined in 2015 using a LabSFLOC (LF), which is a Laboratory Spectral Flocculation Characteristics version of an In-Situ Settling Velocity instrument (INSSEV-LF). Particle characteristics and settling velocities were analyzed from the water column near the surface (sample dp_10 ) and lakebed (sample dp_90 ) at two lake sites (open-lake site ML and littoral site LS01). The term “floc” refers herein to suspended particles that may aggregate or disaggregate to change in size, composition, and settling velocity. During pre-bloom (May) conditions, where maximum suspended particulate matter concentration (SPMC) was 140 milligrams per liter (mg L −1 ) was now observed at site LS01 in close proximity to the bed, where D mean peaked at 305 μm, and the corresponding Ws mean was 3.9 millimeters per second (mm s −1 ). The high near-bed SPMC (828 mg L −1 ) experienced during post-bloom October 2015 at LS01 formed a benthic nepheloid layer (BNL) above the lake’s bed. Numerous low density, fast settling macrofloc-sized organic aggregates (D >160 μm) were observed (some up to 1 mm in size) near bed at LS01 both during the bloom and post-bloom conditions; many of these flocs displayed fibrous organic structures. In terms of mass settling fluxes, the post-bloom BNL produced a total MSF of 4,139 milligrams per square meter per second (mg m −2 s −1 ) (92.1 percent of MSF credited to the macrofloc-sized organic aggregates/cyanobacterial colonies); that was nearly three times the corresponding near-bed settling flux observed during the July 2015 bloom and 360 times greater than the pre-bloom conditions from May 2015 (98.8 percent and 14 percent of MSF credited to the macrofloc-sized fractions for those respective months). Such changes in the near-bed settling flux demonstrate the highly significant seasonal effects that the AFA bloom has on the floc depositional fluxes in UKL and highlights the importance of seasonal monitoring of these conditions in order to correctly parameterize the wide range in depositional characteristics and floc properties measured throughout UKL. Collectively, floc populations observed within UKL demonstrated a wide range in settling velocity (Ws) for a given particle size, D. Similarly, a given settling velocity was not associated with a specific particle size. This variability in particle characteristics and properties indicates the influence of varying floc effective density and its effect on mass and mass settling fluxes (MSF). The use of instruments, such as the INSSEV-LF, enables measuring the variability of settling velocity and its relation to particle density and size.

Oregon↗

USGS2016

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; 2015

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, California. This report includes data collected by U.S. Geological Survey (USGS) scientists for the period from January 2015 to December 2015. These data are appended 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 2015, 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 2015, 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 at the same mudflat 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 (2015), 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 and showed signs of increasing abundance in 2015. 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 an increase in dominance, concurrent with the decrease in Ag and Cu concentrations, 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 abundance in 2015. 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 M. 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 2015 is reflective of species that were available either as pelagic larvae or as mobile adults. Although oviparous (live-birth) 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 2015 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 1970s when the decline in sediment pollutants was the dominating factor.

California↗

USGS2016

Bivalve effects on the food web supporting delta smelt - A long-term study of bivalve recruitment, biomass, and grazing rate patterns with varying freshwater outflow

Executive Summary Phytoplankton is an important and limiting food source in the Sacramento-San Joaquin Delta (the Delta) and San Francisco Bay; the decline of phytoplankton biomass is one possible factor in the pelagic organism decline and specifically in the decline of the protected delta smelt. The bivalves Corbicula fluminea and Potamocorbula amurensis have been shown to control phytoplankton biomass in several locations throughout the system, and their distribution and population dynamics are therefore of great interest. We were able to describe the distribution and dynamics of bivalve biomass through use of samples collected by the California Department of Water Resources (DWR) as part of a monitoring program from 1977 to 2013. As one element of DWR’s and the Bureau of Reclamation’s Environmental Monitoring Program (EMP), the DWR benthic monitoring program examines the impact of water project operations on the estuary as prescribed by a series of Water Rights Decisions mandated by the State Water Resources Control Board (SWRCB). The availability of multidecade samples allowed us to examine long-term trends in biomass, recruitment, and size of bivalves at the 15 stations sampled. Biomass and grazing rate had the same basic trends, and the conclusions that we apply to biomass can be applied to grazing rate data. During winter of most years, Potamocorbula biomass was low at all locations and was near zero in the shallow San Pablo Bay station. The Potamocorbula biomass at shallow stations consistently peaked during summer and fall, but there was no consistent peak season in the deep stations. Corbicula had a much less consistent seasonal biomass pattern than Potamocorbula . However, some interannual patterns were consistent between stations. Corbicula biomass at three stations declined after 2003 (C9, D16, and D28). The Franks Tract (D19) Corbicula biomass had a baseline shift up (that is, all values were > 0) in 1985 until DWR ceased sampling at the station in 1995. Two other stations showed a similar increase in baseline but at different times; D24 shifted up after 2007 and D11 shifted up in 1991. Potamocorbula recruitment (any bivalve ≤ 2.5 millimeters [mm] in length) occurred anytime between spring and fall, with bivalves at the most downstream stations in San Pablo Bay recruiting in spring and animals at the most upstream stations recruiting in fall. The bivalves at the stations between these endpoints recruited in (1) spring or (2) summer and fall (Carquinez Strait), or in some combination of two of those three seasons in Grizzly Bay. The few locations where Potamocorbula and Corbicula overlapped showed recruitment abundance opposing each other, with Potamocorbula recruits peaking during the more saline time of year and Corbicula recruits peaking during periods of lower salinities. Corbicula recruits were present throughout most of the year with some peaks in abundance, but the patterns were not seasonally consistent at any station. Mean size peaked in both bivalves in late summer and early fall and never got above a certain size; maximum size depended on location. The mean size of both bivalves has decreased over the years, with the size distributions throughout the Delta now skewed toward smaller, younger Corbicula (< 10 mm). The mean size of Potamocorbula has also become skewed toward the small, younger bivalves, with sizes in the range of 2 – 8 mm. The mean size of Potamocorbula increased from spring to fall and decreased in winter. A similar generalization is not possible with Corbicula because seasonal patterns in size varied depending on station location. Station D24 on the Sacramento River was the only location with an increase in Corbicula mean size over the sampling period. The largest mean sized Potamocorbula were seen in the channel areas, where sizes of 15 mm were common at stations D41C, 8.1, and D6; sizes in excess of 15 mm were observed at all three D4 stations during the mid 1990s. The mean size of Potamocorbula in the shoals was ≈5 – 7 mm in most years in Grizzly Bay (D7) and San Pablo Bay (D41A), with an increase to > 10 mm at D7 in the wet years. The largest mean sized Corbicula were in the southern Delta (C9 ≈25 mm during 1996 – 97 and 2012 – 2013), and the smallest average sizes were in the San Joaquin River (P8 and D16). Corbicula at the upstream Sacramento River station (D24) and in the southern Delta (C9) showed similar interannual patterns in average size although the animals at C9 were consistently larger than those at D24 were. Corbicula in Franks Tract (D19) and the Old River (D28A) south of Franks Tract were also similar in size and in interannual patterns. At the few stations where Potamocorbula and Corbicula co-occur, it appears that they did not hinder each other’s growth. Both bivalves had large animals at D4, where Corbicula size increased coincident with the presence of Potamocorbula in 1987. Corbicula were observed in wet years prior to Potamocorbula’s invasion at D7 (Grizzly Bay) and were capable of growing to significant size in wet years (> 20 mm in 1986).

California↗