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The escape responses of planktonic copepods to grazing by introduced clams in the San Francisco Estuary were estimated for several copepod species, and resulting loss rates were compared with overall mortality for one species. Experiments were conducted to determine the escape responses of both nauplii and copepodites to entrainment in the siphons of clams ( Potamocorbula amurensis ) and artificial siphons. Copepod nauplii escaped both classes of siphon about 75% of the time and copepodites were more capable of escaping than were nauplii. Escape probabilities were combined with field-based data on clam grazing rates to estimate the impact of clam grazing on copepod survival in the low-salinity region of the San Francisco Estuary. Clams removed nauplii of Eurytemora affinis at a rate of ~ 10% d − 1 with a seasonal pattern from 5% d − 1 in spring to 20% d − 1 in summer–fall and considerable interannual variability. This range of loss rates was similar to the estimated range of total mortality rates for nauplii. Furthermore, the annual estimates of loss rate were negatively correlated with an index of decline in the annual cycle of the copepod population. By combining an understanding of copepod escape capabilities with extensive data on copepod abundance and clam grazing, this paper shows that clam grazing has persisted as a dominant control on the estuarine ecosystem and is implicated in the long-term depression in abundance of food organisms for several fish species that are also in decline.

We estimated the influence of planktonic and benthic grazing on phytoplankton in the strongly tidal, river-dominated northern San Francisco Estuary using data from an intensive study of the low salinity foodweb in 2006–2008 supplemented with long-term monitoring data. A drop in chlorophyll concentration in 1987 had previously been linked to grazing by the introduced clam Potamocorbula amurensis, but numerous changes in the estuary may be linked to the continued low chlorophyll. We asked whether phytoplankton continued to be suppressed by grazing and what proportion of the grazing was by benthic bivalves. A mass balance of phytoplankton biomass included estimates of primary production and grazing by microzooplankton, mesozooplankton, and clams. Grazing persistently exceeded net phytoplankton growth especially for larger cells, and grazing by microzooplankton often exceeded that by clams. A subsidy of phytoplankton from other regions roughly balanced the excess of grazing over growth. Thus, the influence of bivalve grazing on phytoplankton biomass can be understood only in the context of limits on phytoplankton growth, total grazing, and transport.

Dynamic processes (physical, chemical and biological) challenge our ability to quan- tify and manage the ecological risk of chemical contaminants in estuarine environments. Sele- nium (Se) bioavailability (defined by bioaccumulation), stable isotopes and molar carbon-to- nitrogen ratios in the benthic clam Potamocorbula amurensis, an important food source for predators, were determined monthly for 17 yr in northern San Francisco Bay. Se concentrations in the clams ranged from a low of 2 to a high of 22 µg g �1 over space and time. Little of that variability was stochastic, however. Statistical analyses and preliminary hydrodynamic modeling showed that a constant mid-estuarine input of Se, which was dispersed up- and down-estuary by tidal cur- rents, explained the general spatial patterns in accumulated Se among stations. Regression of Se bioavailability against river inflows suggested that processes driven by inflows were the primary driver of seasonal variability. River inflow also appeared to explain interannual variability but within the range of Se enrichment established at each station by source inputs. Evaluation of risks from Se contamination in estuaries requires the consideration of spatial and temporal variability on multiple scales and of the processes that drive that variability.

https://doi.org/10.15447/sfews.2017v15iss2art6The overbite clam (Potamocorbula amurensis) is a major invasive species in the San Francisco Estuary, California, and has been implicated in the decline of pelagic productivity and native fish species. Little is known of its impact on Suisun Marsh, a large brackish tidal region of the estuary. We looked at the abundance and spatial distribution of clams in the marsh, including examining the influence of water quality, using long-term (1988–2015) otter trawl surveys. Temporal trends indicated that overbite clam abundance has been increasing, but adult clams were spatially restricted to a single large slough (Suisun). Clams were absent from most interior channels, limiting their overall effect on the marsh aquatic ecosystem. Abiotic variables, particularly salinity, proved important predictors of overbite clam abundance, although the variables examined alone could not explain overbite clam distributions. We propose that connectivity, detritus loads, and/or predation pressure may work in conjunction with abiotic variables to cause poor survival rates for recruits in interior marsh sites, keeping the distribution limited. Overall results are encouraging for restoration projects in brackish tidal marshes that need to deal with overbite clams.

New Zealand’s current surveillance programme for marine pests does not include methods for identification of organisms in the water column, therefore dispersive forms go undetected. Molecular methods provide an opportunity to detect dispersive forms thereby contributing to a more robust surveillance programme. Additionally, New Zealand has become a signatory to the IMO Ballast Water Convention and there is scope for developing enumeration methods for detection of viable organisms as well as species-specific molecular probes for indicator bacteria. We describe here the outcome of experiments testing the effects of various matrices (e.g. sediment, biofilms, benthic assemblage, seawater) against a quantitative PCR (QPCR) assay developed for Potamocorbula amurensis. The limit of detection of the assay for sediments and benthic assemblages ranged between one to five larvae per 10 g wet weight. We also report a QPCR assay for Vibrio cholerae, one of the indicator species in the Ballast Water Convention. Quantitative PCR of seawater spiked with different concentrations of culture showed that assay sensitivity was insufficient to detect the regulatory limit of 1 colony forming unit (CFU) per 100 mL. More recent work suggests that sufficient sensitivity can be achieved with cultivation based methods (most probable number-QPCR [MPN-QPCR]). We are currently appraising several multispecies detection methods including micro-arrays and next generation sequencing for their suitability in marine pest detection. The advantages and disadvantages of each are discussed herein. We highlight the need to consider issues relating to sampling design when using molecular methods for surveillance and compliance monitoring.

The ability of bivalve filter feeders to limit phytoplankton biomass in shallow waters is well-documented, but the role of bivalves in shaping phytoplankton communities is not. The coupled effect of bivalve grazing at the sediment-water interface and sinking of phytoplankton cells to that bottom filtration zone could influence the relative biomass of sinking (diatoms) and non-sinking phytoplankton. Simulations with a pseudo-2D numerical model showed that benthic filter feeding can interact with sinking to alter diatom:non-diatom ratios. Cases with the smallest proportion of diatom biomass were those with the fastest sinking speeds and strongest bivalve grazing rates. Hydrodynamics modulated the coupled sinking-grazing influence on phytoplankton communities. For example, in simulations with persistent stratification, the non-sinking forms accumulated in the surface layer away from bottom grazers while the sinking forms dropped out of the surface layer toward bottom grazers. Tidal-scale stratification also influenced vertical gradients of the two groups in opposite ways. The model was applied to Suisun Bay, a low-salinity habitat of the San Francisco Bay system that was transformed by the introduction of the exotic clam Potamocorbula amurensis. Simulation results for this Bay were similar to (but more muted than) those for generic habitats, indicating that P. amurensis grazing could have caused a disproportionate loss of diatoms after its introduction. Our model simulations suggest bivalve grazing affects both phytoplankton biomass and community composition in shallow waters. We view these results as hypotheses to be tested with experiments and more complex modeling approaches.

Silica distributions in estuaries can be used to infer uptake, particularly that due to production by diatoms. I used data from two long-term monitoring programs to infer long-term patterns of diatom production during summer in the river-dominated northern San Francisco estuary. This region was most heavily affected by grazing by the clam Potamocorbula amurensis,introduced in 1986. Production based on dissolved silica (Dsi) uptake was high during the 1970s and early 1980s except during a drought in 1976‐1977. From 1987 to 2002 production averaged 1% and 17% of the preclam values from the two monitoring programs. Low values in 1976‐1977 and after 1986 are consistent with a loss of diatom production due to benthic grazing. There is no evidence of a relation between DSibased production and either freshwater flow or temperature, and therefore climate change is an unlikely influence on the long-term trend in diatom production in this part of the estuary. Primary production calculated from chlorophyll and extinction coefficient was of a similar magnitude to that calculated from DSi depletion, indicating that most production was due to diatoms during summers of the preclam period.

In many estuaries worldwide, climate trends together with human diversion of fresh water have dramatically impacted the benthos. Such impacts have sometimes been complicated by exotic species, whose invasion and persistence can be mediated by wide variations in freshwater inflow. Monitoring such changes usually involves periodic samples at a few sites; but sampling that does not recognize variation at a range of spatial and seasonal scales may not reveal important benthic trends. San Pablo Bay, in northern San Francisco Bay, has extreme fluctuations in freshwater inflow. This bay also experienced a major benthic change with introduction of the Asian clam (Potamocorbula amurensis) in 1986. This species initially displaced the former community, but later appeared to vary in abundance depending on site and freshwater inflow. To investigate such patterns and provide guidelines for research and monitoring, we took 1746 core samples at six sites around San Pablo Bay from 19 October to 17 December 1999 and from 6 March to 19 April 2000. Most biomass consisted of the clams P. amurensis, Macoma balthica and Mya arenaria. Potamocorbula amurensis dominated the benthos at most sites in the fall and recruited a new cohort during winter, while there was weak recruitment in M. balthica and none in M. arenaria. At most but not all sites, densities of P. amurensis and M. arenaria declined dramatically over winter while M. balthica declined only slightly. The dominant clams had patch diameters O5 m at most but not all sites, and some showed inconsistent patch structure at scales of 100e1400 m. In this semiarid estuary with highly variable freshwater inflow, samples for research and monitoring should include multiple sites and seasons, and samples within sites should be R5 m apart to account for between-patch variation. Species abundance in winter 1999e2000 appeared to be affected by high freshwater inflows in 1997e1999, while spatial patterns were probably most affected by post-settlement dispersal and mortality. 2003 Elsevier Ltd. All rights reserved.

Cm Respiration and calcium carbonate production by the invasive Asian clam, Potamocorbula amurensis, were cal­ culated to assess their importance as CO2 sources in northern San Francisco Bay. Production, calculated using monthly population density and size structure measured at three sites over 7 yr and a shell length/CaCO3 conversion factor, averaged 221 (�184) g CaCO3 m �2 yr �1 . Net calcium carbonate production by this exotic bivalve releases CO2 at a mean rate of 18 (�17) g C m �2 yr �1 . Respiration by P. amurensis, estimated from secondary production, releases additional CO2 at a mean rate of 37 (� 34) gCm �2 yr �1 . Therefore, total net CO2 production by P. amurensis averages 55 (�51) g C m �2 yr �1 in an estuarine domain where net primary production consumes only 20 g inorganic �2 yr �1 .C O 2 production by P. amurensis in northern San Francisco Bay is an underestimate of the total CO2 supply from the calcified zoobenthic communities of San Francisco Bay, and results from other studies have sug­ gested that this rate is not unusual for temperate estuaries. Global extrapolation yields a gross CO2 production rate in the world's estuaries of 1 � 10 14 gCy r �1 , which suggests that calcified benthic organisms in estuaries generate CO2 equal in magnitude to the CO2 emissions from the world's lakes or from planetary volcanism (the net source is determined by the highly variable rate of CO2 consumption by carbonate dissolution). This biogenic CO2 source is increasing because of the continuing global translocation of mollusks and their successful colonization of new habitats.

We compared dietary patterns within a temperate estuarine fish assemblage (Suisun Marsh, CA, U.S.A.) during a period of high mysid shrimp abundance and after a major decline in mysid abundance caused by the invasion of the overbite clam Potamocorbula amurensis. Prior to the invasion, high dietary overlap, high stomach fullness, and low niche breadth occurred among the fishes in spring when mysid populations were high. Dietary overlaps decreased and niche breadth increased for all species but the endemic splittail Pogonichthys macrolepidotus in fall when mysid populations were low. Eight native species exhibited lower overall collective overlaps and fuller stomachs than five alien species, suggesting more efficient resource partitioning. After mysid abundance declined, only alien striped bass Morone saxatilis preyed upon mysids in greater than trace amounts. An alien mysid became an important prey for small striped bass, but striped bass also switched to piscivory at a smaller size than when mysids were abundant. Eight of 13 species exhibited significant declines in abundance during the study period, which were concordant with the original importance of mysids in their diets. Our results suggest that altered lower food web dynamics in the San Francisco Estuary caused by the invasion of the overbite clam changed fish diets and have contributed to declines in fish abundance.

This paper examines how the subcellular partitioning of Cd and Zn in the bivalves Macoma balthica and Potamocorbula amurensis may affect the trophic transfer of metal to predators. Results show that the partitioning of metals to organelles, 'enzymes' and metallothioneins (MT) com- prise a subcellular compartment containing trophically available metal (TAM; i.e. metal trophically available to predators), and that because this partitioning varies with species, animal size and metal, TAM is similarly influenced. Clams from San Francisco Bay, California, were exposed for 14 d to 3.5 µg l -1 Cd and 20.5 µg l -1 Zn, including 109 Cd and 65 Zn as radiotracers, and were used in feeding experiments with grass shrimp Palaemon macrodatylus, or used to investigate the subcellular parti- tioning of metal. Grass shrimp fed Cd-contaminated P. amurensis absorbed ~60% of ingested Cd, which was in accordance with the partitioning of Cd to the bivalve's TAM compartment (i.e. Cd asso- ciated with organelles, 'enzymes' and MT); a similar relationship was found in previous studies with grass shrimp fed Cd-contaminated oligochaetes. Thus, TAM may be used as a tool to predict the trophic transfer of at least Cd. Subcellular fractionation revealed that ~34% of both the Cd and Zn accumulated by M. balthica was associated with TAM, while partitioning to TAM in P. amurensis was metal-dependent (~60% for TAM-Cd%, ~73% for TAM-Zn%). The greater TAM-Cd% of P. amuren- sis than M. balthica is due to preferential binding of Cd to MT and 'enzymes', while enhanced TAM- Zn% of P. amurensis results from a greater binding of Zn to organelles. TAM for most species-metal combinations was size-dependent, decreasing with increased clam size. Based on field data, it is esti- mated that of the 2 bivalves, P. amurensis poses the greater threat of Cd exposure to predators because of higher tissue concentrations and greater partitioning as TAM; exposure of Zn to predators would be similar between these species.

Many aspects of metal accumulation in aquatic invertebrates (i.e. toxicity, tolerance and trophic transfer) can be understood by examining the subcellular partitioning of accumulated metal. In this paper, we use a compartmentalization approach to interpret the significance of metal, species and size dependence in the subcellular partitioning of Cd and Zn in the bivalves Macoma balthica and Potamocorbula amurensis. Of special interest is the compartmentalization of metal as metal- sensitive fractions (MSF) (i.e. organelles and heat-sensitive proteins, termed 'enzymes' hereafter) and biologically detoxified metal (BDM) (i.e. metallothioneins (MT) and metal-rich granules (MRG)). Clams from San Francisco Bay, CA, were exposed for 14 d to seawater (20 ‰ salinity) containing 3.5 µg l -1 Cd and 20.5 µg l -1 Zn, including 109 Cd and 65 Zn as radiotracers. Uptake was followed by 21 d of depuration. The subcellular partitioning of metal within clams was examined following exposure and loss. P. amurensis accumulated ~22 × more Cd and ~2 × more Zn than M. balthica. MT played an important role in the storage of Cd in P. amurensis, while organelles were the major site of Zn accu- mulation. In M. balthica, Cd and Zn partitioned similarly, although the pathway of detoxification was metal-specific (MRG for Cd; MRG and MT for Zn). Upon loss, M. balthica depurated ~40% of Cd with Zn being retained; P. amurensis retained Cd and depurated Zn (~40%). During efflux, Cd and Zn concentrations in the MSF compartment of both clams declined with metal either being lost from the animal or being transferred to the BDM compartment. Subcellular compartmentalization was also size-dependent, with the importance of BDM increasing with clam size; MSF decreased accordingly. We hypothesized that progressive retention of metal as BDM (i.e. MRG) with age may lead to size dependency of metal concentrations often observed in some populations of M. balthica.

We describe a laboratory investigation into the effect of turbulent hydrodynamic stresses on clam larvae in the settlement phase of the recruitment process. A two-component laser-Doppler anemometer (LDA) was used to measure time histories of the instantaneous turbulence structure at potential recruitment sites within reconstructed beds of the adult Asian clam, Potamocorbula amurensis.Measurements were made for two flow speeds over beds with three different clam densities and two different clam heights. We analyze the statistical effect of the turbulence on the larval flux to the bed and on the probability of successful anchoring to the substrate. It is shown that the anchoring probability depends on the nature of the instantaneous stress events rather than on mean stresses. The instantaneous turbulence structure near the bed is altered by the flow rate and the spacing and height of adult clams living in the substrate. The ability to anchor quickly is therefore extremely important, since the time sequence of episodic turbulent stress events influences larval settlement success. The probability of successful larval settlement is predicted to decrease as the spacing between adults decreases, implying that the hydrodynamics impose negative feedback on clam bed aggregation dynamics. Species success, population density, and community structure are all dependent on larval recruitment. Therefore, the processes of settlement and recruitment of benthic and epibenthic communities have been the subject of substantial research (see Olafsson et al. 1994; Wildish and Kristmanson 1997 for recent reviews). A major portion of the work has involved the transport of larvae to the bed and settling of the larvae by passive or active selection processes ( see reviews by Butman 1987; Abelson and Denny 1997). Several researchers have found that it is the combination of larval behavior (e.g., swimming, crawling, burrowing) and physical processes that deliver the larvae to the bed that is responsible for the recruitment success (Mullineaux and Butman 1990; Butman and Grassle 1992; Grassle et al. 1992; Snelgrove et al. 1993). As summarized by Underwood and Keough (2001), it is no longer a question of whether hydrodynamics or behavior are important in recruitment, rather it is a question of ‘‘under which conditions is larval behavior important?’’ We will expand this question and say that it is also important to determine the periods, during the relevant physical processes, when larval behavior is important. Related to the interest in larval recruitment is an ecological interest in what regulates temporal, spatial, and agesegregated distributions of species. Thus, the processes important in determining how aggregations of benthic 1

Although nutrient supply often underlies long-term changes in aquatic primary production, other regulatory processes can be important. The Sacramento‐San Joaquin River Delta, a complex of tidal waterways forming the landward portion of the San Francisco Estuary, has ample nutrient supplies, enabling us to examine alternate regulatory mechanisms over a 21-yr period. Delta-wide primary productivity was reconstructed from historical water quality data for 1975‐1995. Annual primary production averaged 70 g C m 22 , but it varied by over a factor of five among years. At least four processes contributed to this variability: (1) invasion of the clam Potamocorbula amurensis led to a persistent decrease in phytoplankton biomass (chlorophyll a) after 1986; (2) a long-term decline in total suspended solids—probably at least partly because of upstream dam construction—increased water transparency and phytoplankton growth rate; (3) river inflow, reflecting climate variability, affected biomass through fluctuations in flushing and growth rates through fluctuations in total suspended solids; and (4) an additional pathway manifesting as a long-term decline in winter phytoplankton biomass has been identified, but its genesis is uncertain. Overall, the Delta lost 43% in annual primary production during the period. Given the evidence for food limitation of primary consumers, these findings provide a partial explanation for widespread Delta species declines over the past few decades. Turbid nutrient-rich systems such as the Delta may be inherently more variable than other tidal systems because certain compensatory processes are absent. Comparisons among systems, however, can be tenuous because conclusions about the magnitude and mechanisms of variability are dependent on length of data record.

All ecosystems are influenced by physical forcing. Estuarine ecosystems respond most strongly on an interannual timescale to variability in freshwater flow. Several mechanisms for positive or negative flow effects on biological populations in estuaries have been proposed; however, positive effects appear to operate mainly through stimulation of primary production with effects propagating up the food web. In the northern San Francisco Estuary, abundance or survival of several common species of fish and shrimp varied positively with flow-in data through 1992. I re-examined these relationships and those of several additional taxa in an analysis of long-term (20 to 40 yr) mon- itoring data. The spread of the introduced clam Potamocorbula amurensis in 1987 provided an oppor- tunity to examine simultaneously the responses of estuarine species to flow and to changes in the food web. I separated variability into a flow response, a step change after 1987 and other sources of variability. Responses of fish and shrimp contrasted with those of lower trophic levels. All but 1 spe- cies of nekton responded positively to flow, only 2 had clear declines after 1987, and none of the rela- tionships changed in slope after 1987. In contrast with the higher trophic levels, chlorophyll a (chl a) and several species of zooplankton declined markedly after 1987, and had either weak responses to flow or responses that changed after 1987. Thus, the food web appears strongly coupled between benthos and plankton, and weakly coupled between zooplankton and fish, as has been found in other systems. More importantly, the variation with freshwater flow of abundance or survival of organisms in higher trophic levels apparently did not occur through upward trophic transfer, since a similar rela- tionship was lacking in most of the data on lower trophic levels. Rather, this variation may occur through attributes of physical habitat that vary with flow.

Phytoplankton are an important source of selenium (Se) for aquatic invertebrates, which accumulate Se primarily through dietary ingestion. The extent to which Se bioavailability varies among different phytoplankton species could help explain different bioaccumulation patterns observed for invertebrates in nature. We measured the efficiency with which 3 benthic invertebrates assimilated 75 Se from 5 phytoplankton species using standard pulse-chase techniques. The inverte- brates included the amphipod Leptocheirus plumulosus and the bivalves Macoma balthica and Pota- mocorbula amurensis. The phytoplankton species included Cryptomonas sp. (Cryptophyceae), Gymnodinium sanguinem (Dinophyceae), Phaeodactylum tricornutum (Bacillariophyceae), Syne- chococcus sp. (Cyanophyceae) and Thalassiosira pseudonana (Bacillariophyceae). The range of Se assimilation efficiency (AE) by L. plumulosus (32.1 ± 1.8 to 69.5 ± 7.1%) was the lowest of the 3 organ- isms. No relationship was observed between the proportion of Se in algal cell cytoplasm and Se AE by L. plumulosus, which is consistent with findings for assimilation of other trace elements by this organism. Se AE by M. balthica (range: 58.0 ± 3.2 to 92.3 ± 6.0%) varied according to the proportion of cytoplasmic Se in algal cells (p < 0.0001, r 2 = 0.868). P. amurensis assimilated between 78.3 ± 2.0 and 88.9 ± 3.6% of Se from algal cells, and the relationship between cytoplasmic Se and Se AE was described by the following equation: Se AE = 69.2 + 0.22 · (% cytoplasmic Se) (p = 0.003, r 2 = 0.405). This relationship suggests that P. amurensis assimilated non-cytoplasmic Se from phytoplankton, perhaps through utilization of the glandular digestive pathway. Consistently high Se assimilation from algae by P. amurensis may contribute to elevated Se concentrations observed for this organism.

Corbula gibba (Olivi, 1792) a small exotic bivalve from the eastern Atlantic and the Mediterranean has been present in Port Phillip Bay, Victoria, Australia, from as early as 1987. C. gibba is widespread, abundant, and possesses characteristics such as fast growth which may confer a competitive advantage over endemic species like the commercial scallop Pecten fumatus Reeve, 1855. Experimental manipulations in the field showed that ambient densities of C. gibba significantly affected the size and growth of juvenile P. fumatus. This effect was greater than the effect of an equivalent number of conspecific scallops. C. gibba did not, however, affect scallop condition or survival in the short term, although the power of the test to detect a 50% decrease in survival was low. The percentage of experimental scallops lost to different sources of mortality was also unaffected by the presence of C. gibba, as was the density of predators found in experimental enclosures. This study is the first to experimentally demonstrate the impact of an introduced marine mollusc on an endemic species in Australia. A possible mechanism underlying this impact is compe- tition for food, as both species are suspension feeders which live in an environment where resource limitation may occur.

Multi-year investigations in northern San Francisco Bay by United States Geological Survey have linked reduced condition indices in populations of Asian clam (Potamocorbula amurensis) with elevated cadmium tissue concentrations. Our study seeks to determine whether levels of hsp70 proteins in P. amurensis can be correlated with these findings, and/or are related to histopathologic alterations and concentrations of metallothionein-like proteins. Here we present our results on stress proteins in clams collected monthly from four field stations between July 1996 and January 1998. In addition, animals were exposed in the laboratory to a range of salinities. Stress proteins were analyzed by Western blotting using monoclonal antibodies. Hsp70 protein levels in field-collected clams were significantly higher at the seaward (high salinity/low cadmium) stations (12.5, 8.1) than at the landward (low salinity/high cadmium) stations (6.1, 4.1). Laboratory studies showed that clams exposed to 0.1 ppt salinity had markedly lower hsp70 levels than clams exposed to higher salinities. In view of our previous laboratory studies showing that cadmium induces hsp70 in P. amurensis, our present results indicate that reduced hsp70 protein levels in field-collected clams may be linked to salinity effects rather than cadmium tissue concentrations.

Previously, we have shown that Asian clams (Potamocorbula amurensis) with highest metallic body burdens have highest prevalence of disease and lowest reproduction. The present study was designed to assess and validate potential sublethal toxicity of hexavalent chromium (Cr-VI) in clams under controlled laboratory exposure. For 7 days, three replicates of clam (n = 10 per replicate) were exposed to aqueous solution containing 0.00, 0.92, 8.40, or 25.6 mg l-1 of Cr-VI at 15 degrees C and 15 g l-1 salinity. Mortality reached 100% in the 25.6 mg l-1 group within 7 days. There was no significant difference in mortality among the control, 0.92, and 8.40 mg l-1 groups. Western blot analyses revealed significantly elevated stress protein hsp70 levels in the 8.40 mg l-1 treatment group. Histopathologic analyses revealed mild digestive gland (DG) atrophy in the control group. Clams exposed to 0.92 mg l-1 Cr-VI showed moderate DG atrophy, moderate granulomatous inflammation and necrosis in DG, ovary and testis. Lesions observed in the 8.40 mg l-1 treatment group included severe DG atrophy, severe granulomatous inflammation and necrosis in byssal gland, DG, gill, kidney, ovary and testis. In gills and testes of treated groups, apoptotic cells outnumbered mitotic cells. In addition, gills from clams in the 8.40 mg l-1 group showed enhanced hsp70 staining. Our studies support a cause-effect relationship between contaminants and reduced health in Asian clams and indicate the DGs, gills, and reproductive organs are principal targets of Cr-VI toxicity at sublethal concentrations. Results from this study suggest that Cr-VI may have played a role in the increased incidence of diseased clams seen in previous studies and these adverse effects may be working to decrease clam populations at sites with highest metallic contamination in the San Francisco Bay Estuary.

The US Geological Survey has reported the presence of a metal contamination gradient in clam tissues, decreased condition indices, and irregular reproductive patterns have been reported in the Asian clam, Potamocorbula amurensis, from San Francisco Bay. If metals are driving the observed patterns in the field, then biomarkers of exposure, and possibly deleterious effect, should show a corresponding gradient. In this study, biomarkers from sub-cellular to tissue levels of biological organization were assessed in P. amurensis collected from the Bay or exposed to cadmium in the laboratory. Cellular and tissue alterations were assessed using histopathology and enzyme histochemistry (EH). Alterations in the ovary, testis, kidney, and gill tissues were most common at the most contaminated station when data were averaged over a 12-month sampling period. EH analysis indicated decreased active transport, energy status, and glucose oxidation in kidney and digestive gland at the most contaminated site which may indicate a decreased potential for growth. Ovarian lesions observed in feral Asian clams were experimentally induced in healthy clams by cadmium exposure in laboratory exposures. Our results suggest a contaminant etiology for tissue alterations.

Particle digestion in lamellibranch bivalves is partitioned between 2 paths, an 'intestinal' path through the stomach and intestine and a 'glandular' path through the stomach, digestive gland and intestine. In the Asian clam Potamocorbula amurensis (Schrenck, 1867), the relative importance of the intestinal path increases compared to the glandular path as food availability and ingestion rate increases. The effects of changes in food availability and ingestion rate on digestive partitioning are at least as important as the effect of changes in diet observed by other investigators. Analyses of residence-time distributions of inert 9 and 44 pm particle tracers show that the gut of P amurensis can be modeled as an ideal mixing reactor (stomach and digestive gland) and an ideal plug-flow reactor (intestine) in series. This model appears to be valid for the processing of particles ≤ 9 μm in size. For particles of ≥15 μm, the ideal mixing component of the model must be modified to account for channeling of particles through the stomach to the intestine. Larger particles can enter the digestive gland, but are probably not phagocytized for intracellular digestion. Instead they may clog the ducts and tubules, limiting phagocytosis of smaller particles and potentially reducing the extent of digestion and absorption. Mixing, and the resultant intragut particle-sorting thus appear to be necessary components of a digestive strategy that incorporates intracellular digestion.

Studies of butyltin compounds in soil, benthic sediments and the Asian clam Potamocorbula amurensis were conducted at the former Mare Island Naval Shipyard, and nearby Mare Island and Carquinez Straits in San Francisco Bay, California. Soils from a sandblast abrasives dump site at the shipyard contained low concentrations of mono-, di- and tributyltin (0.3–52 ng/g, total butyltin). Similarly, concentrations of total butyltin in benthic sediments from nearby Mare Island and Carquinez Straits ranged from 1.3 to 8.1 ng/g. In contrast, clams accumulated much greater concentrations (152–307 ng/g, total butyltin). Tributyltin (TBT) and dibutyltin (DBT) made up from 54–85% to 15–46%, respectively, of the total butyltin body burden of the clams. Biota Sediment Accumulation Factors (BSAFs) for butyltins in Potamocorbula were in reasonable agreement with literature values; they are greater than those of neutral hydrophobic compounds, suggesting that partitioning and binding processes may be involved in bioaccumulation. Tributyltin is a potent endocrine disrupting chemical. There is potential for long-term chronic effects of TBT in San Francisco Bay.

Stable C and N isotope measurements of the clam Potamocorbula amurensis were used to help identify watershed-level differences in food webs of San Francisco Bay. Potamocorbula amurensis has become widely distributed in San Francisco Bay since introduction from Asia in1986. Clam samples were collected from both the river-influenced northern arm of San Francisco Bay and the lagoonal southern arm of the Bay during 1990-1991. Carbon isotopic compositions of clams responded primarily to riverine inputs and provided an index of hydrologic mixing across the estuarine system. Nitrogen isotopic compositions of clams were more responsive to watershed nutrient loading, with higher δ15N values found in South Bay, which receives stronger inputs of anthropogenic N. Routine monitoring of animal consumer isotopic compositions could be an effective way to detect long-term watershed-level changes in C and N dynamics important for secondary production in aquatic systems.

In many estuaries, maxima in turbidity and abundance of several common species of zooplankton occur in the low salinity zone (LSZ) in the range of 0.5–6 practical salinity units (psu). Analysis of zooplankton abundance from monitoring in 1972–1987 revealed that historical maxima in abundance of the copepod Eurytemora affinis and the mysid Neomysis mercedis, and in turbidity as determined from Secchi disk data, were close to the estimated position of 2 psu bottom salinity. The copepod Sinocalanus doerrii had a maximum slightly landward of that of E. affinis. After 1987 these maxima decreased and shifted to a lower salinity, presumably because of the effects of grazing by the introduced clam Potamocorbula amurensis. At the same time, the copepod Pseudodiaptomus forbesi, the mysid Acanthomysis sp., and amphipods became abundant with peaks at salinity around 0.2–0.5 psu.

The bioavailability to clams (Potamocorbula amurensis and Macoma balthica) of Cd, Cr, and Zn from suspended particulate material (SPM) collected during a phytoplankton bloom was compared to bioavailability from SPM dominated by resuspended sediments. Bioavailability was also compared among mudflat sediments amended with different levels of living benthic microalgae. Bioavailability was defined by absorption efficiencies determined using pulse-chase protocols, modified for studying natural particle assemblages. The partitioning of Cd and Zn to particles (&) increased as the microalgae biomass (Chl a) increased in the particle assemblages; partitioning of Cr was less affected by the algal biomass. The clams fed particle assemblages enriched with microalgae absorbed Cd and Zn with significantly greater efficiency than did the clams fed algae-poor particles. This was partially explained by the greater occurrence of Cd and Zn in the cytosolic fraction of the particle assemblages that were microalgae enriched, as well as by the efficient absorption of cytosolic material by the clams. Among metals, Zn was most efficiently absorbed by both clams, and Cr the least. M. balthica absorbed Zn more efficiently from all types of food particles (39-82%) than did P. amurensis (13-50%). P. amureasis absorbed Cd with greater efficiency from the bloom SPM (44-48%) than did M. balthica (13-21%), but the two clams absorbed Cd similarly from benthic microalgae (26 51%). The addition of microalgae to complex natural particle assemblages clearly affected the bioavailability of associated metals, so studies using sediments (or suspended particulate material) that do not include a realistic living food component could underestimate metal bioavailability from particle ingestion.

Radiotracer studies were employed to quantitatively compare the biokinetics of uptake from the dissolved phase (influx rates) and loss (efflux) between 2 bivalves, Potamocorbula amurensis and Macoma balthica, and among the metals Cd, Cr and Zn. Effects of salinity on influx rate were evaluated in these 2 highly euryhaline species as were effects of animal size on uptake and loss. Metal speciation and biological attributes interacted to differentiate bioaccumulation processes among metals and between species. Influx rates of the 3 metals (pg g-' (dry wt) d-') increased linearly with dissolved metal concentrations. Influx rates of Zn in both clams were 3 to 4x those for Cd and 15x those for Cr. However, influx on the basis of free ion activities would be faster for Cd than for Zn. Relative influx rates among the metals were similar in the 2 bivalves. But, absolute influx rates of all 3 metals were 4 to 5x greater in P. amurensis than in M, balthica, probably because of differences in biological attrib- utes (i.e. clearance rate or gill surface area). As salinity was reduced from 30 to 5 psu, the influx rate of Cd for P. amurensis increased 4-fold and that for M, balthica increased 6-fold, consistent with expected changes in speciation. However the influx rates of Cr in both clams also increased 2.4-fold over the same range, indicating a biological contribution to the salinity effect. Influx rates of Zn were not sig- nificantly affected by salinity. Weight specific metal influx rates (pg g-' (dry wt) d-') were negatively correlated with the tissue dry weight of the clams, but most rate constants determining physiological turnover of assimilated metals were not affected by clam size. The exception was the rate constant for Cd loss, which resulted in faster turnover in large M. balthica than in smaller clams. The rate constant of loss for P. amurensis increased in the order of Cd (0.011 d-') < Zn (0.027 d-') < Cr (0.048 d-'). This was different from the hierarchy of rate constants for M. balthica: Zn (0.012 d-I) < Cd (0.018 d-I) < Cr (0.024 d-').

Pulse-chase experiments show that two ma- rine bivalves take optimal advantage of different types of particulate food by varying food retention time in a flexible two-phase digestive system. For example, carbon is effi- ciently assimilated from bacteria by subjecting nearly all the ingested bacteria to prolonged digestion. Prolonging digestion also enhances assimilation of metals, many of which are toxic in minute quantities if they are biologically available. Detritus-feeding aquatic organisms have always lived in environments naturally rich in particle-reactive metals. We suggest that avoiding excess assimilation of metals could be a factor in the evolution of digestion strat- egies. We tested that suggestion by studying digestion of particles containing different Cr concentrations. We show that bivalves are capable of modifying the digestive pro- cessing of food to reduce exposure to high, biologically available, Cr concentrations. The evolution of a mecha- nism in some species to avoid high concentrations of metals in food could influence how effects of modern metal pol- lution are manifested in marine ecosystems.

Multiple indicators (Chl a, C : N ratios, [6L3C]POC, and two classes of lipid biomarker compounds- sterols and phospholipid ester-linked fatty acids) were used to evaluate spatial and temporal variations in the origin of particulate organic matter (POM) in the San Francisco Bay (SFB) estuary. Comparisons were made between the northern and southern subestuaries of SFB, as well as along the salinity gradient of northern SFB. Two sample types were collected-seston, which was used to characterize the bulk POM, and tissues of the suspension-feeding bivalve Potamocorbula amurensis -in order to evaluate the assimilable portion of the POM. Samples were collected around biological and physical events (phytoplankton blooms and freshwater inflow) thought to be the primary mechanisms controlling temporal variability in organic matter sources. Seston samples indicate that phytoplankton sources of POM are important throughout the entire SFB system, with additional inputs of organic matter from bacterial and terrestrial vascular plant sources delivered to the northern region. Analysis of biomarker compounds in- P. amurensis tissues indicates that phytoplankton supply a large fraction of the assimilable carbon to clams throughout SFB, although isotopic analysis of clam tissues suggests that the origin of this reactive carbon varies spatially and that freshwater algae are an important source of reactive organic matter to clams living in northern SFB.

ABSmCT: potamocorbula emurensis was assessed as a biosentinel species in San Francisco Bay, Cal- , ifornia, USA. Uptake of metal in both the laboratory and field showed that P. amurensis was suffiaently responsive to ~g, Cd, Cr, Ni and V to detect environmental differences in exposure. It was less suitable as an indicator of Cu and Zn contamination. Concentration fadon for P. amurensir were: Ag, 386000; Cd, 50200;Cr, 36600;Cu, 12200;Ni. 5200;and Zn, 115500.Samples were collected from 6 stations throughout the bay at near-monthly intervals from January 1991 to March 1992. Variability within a collection was influenced by gut content and animal size. Other sources of variability were time [coefficient of variation (CV) = 10 to 21 %], small-scale spatial variability (within 3 Irm,CV = 10 to 25 %), and large-scale spatial variability (CV = 3.3 to 12.4 %). Depuration for 48 h was necessary to mitigate bias from gut content. Precision was improved by analyzing large numbers of individuals (60to 120)separated into several (5 to 14)composites at each collection and by determining, from regression, the mean and variance for samples with significant correlations between metal concentration and shell length. Repeated monthly sampling inaeased the accuracy of long-term site characterizations. Temporal variability was small because of drought. The grand means of the concentrations of Ag, Cd, Cr, Ni, and V in the tissues of P. amurensis at each station for the 15 mo period revealed persistent contamination from industrialized Suisun Bay to the mouth of San Franasco Bay. Demonstration of responsiveness. precision and accuracy should be a prerequisite for the optimal use of biosentinels.

The genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay was described using starch gel electrophoresis at eight presumptive loci. Specimens were taken from five environmentally distinct sites located throughout the bay. The population maintains a high degree of genetic variation, with a mean heterozygosity of 0.295, a mean polymorphism of 0.75, and an average of 3.70 alleles per locus. The population is genetically homogeneous, as evidenced from genetic distance values and F-statistics. However, heterogeneity of populations was indicated from a contingency chi-square test. Significant deviations from Hardy-Weinberg equilibrium and heterozygote deficiencies were found at the Lap-1 locus for all populations and at the Lap-2 locus for a single population. High levels of variability could represent a universal characteristic of invading species, the levels of variability in the source population(s), and/or the dynamics of the introduction. Lack of differentiation between subpopulations may be due to the immaturity of the San Francisco Bay population, the “general purpose” phenotype genetic strategy of the species, high rates of gene flow in the population, and/or the selective neutrality of the loci investigated.

The clam Potamocorbula amurensis was introduced into the San Francisco Bay estuary (California, USA) in 1986 and became abundant in late 1987. Within a year, chlorophyll concentration and the abundance of adults of 3 common estuarine copepod species had declined by 53 to 91 %, providing an opportunity to examine mechanisms by which benthic grazing might control the abundance of pelagic populations. Declines in chlorophyll and abundance of the 3 species of copepod coincided approximately with the geographic range of the clam population. The decline in abundance of the copepod Eurytemora affinis was accompanied by a decrease in the ratio of nauplii to adults, but not in the ratio of eggs to females. Therefore, the decline in abundance may be due to elevated mortality of nauplii rather than food limitation of reproductive rate. We argue that direct predation by P. amurensis is the cause of the reduced sunrival of nauplii, and therefore of the depressed abundance of adults. Experimentally determined clearance rates of P. amurensis on E. affins nauplii averaged 0.11 1 clam-' d-'. If that clearance rate applied in the field, the clams could remove 8.2% of the nauplii d-I. This removal rate is sufficient to explain the observed rate of population decline. P. amurensis appears to have become well established, and copepod populations of the bay so far have failed to rebound. Thus this invasion may have permanent effects. In a broader sense, predation on zooplankton by soft-bottom benthos may be an important, and heretofore overlooked, source of mortality in shallow waters. Selectivity occurring through differences in escape response and vertical position could make bivalve predation an important influence on biomass and species composition of inshore zooplankton.

This study compared clearance and assimilation of natural bacterioplankton (< 1.2 pm) and cultured phytoplankton by an Asian bivalve, Potamocorbula amurensis. The average clearance rate for bacterioplankton was 45 ml h-l clam-’ and was independent of the size (shell length, wet wt including shell, or dry tissue wt) of the clam. The clearance rate for phytoplankton is given byf = 162 + 166 x WW orf = -40 + 199 x L whereJ; WW, and L are clearance rate (ml h-l), wet weight including shell (g), and shell length (cm). Bacteria were readily assimilated by P. amurensis. Gross assimilation was 73% after 49 h compared to 90% for Isochrysis galbana. Net assimilation was 45 and 53% for bacterioplankton and I. galbana, respectively. Bacterial carbon appeared to be respired faster than algal carbon. As seen in other bivalves, feces production increased and assimilation efficiency decreased at higher food concentrations. At the mean bacterioplankton and phytoplankton standing stocks found in northern San Francisco Bay, bacteria supplied - 13 and 16% of the sum of bacteria and phytoplankton C and N, respectively, consumed by a 1 -cm P. amurensis. We calculate that a 1 -cm clam could double its C biomass in 22 1 d by feeding on bacterioplankton and in 26 d by feeding on phytoplankton.

The recent invasion of San Francisco Bay by the suspension-feeding clam Putamocorbula amurensis has provided an opportunity to document the ecological consequences of a major biological disturbance. Previous work over the last two decades has shown that phytoplankton biomass in the upper estuary is low (2-3 mg Chl a m-3) during seasonal periods of high river flow and short residence time, and it is usually high (peak > 30 mg Chl a m-3) during the summer-autumn seasons of low river flow and long residence time. However since P. amurensis became widespread and abundant in 1987, the summer phytoplankton biomass maximum has disappeared, presumably because of increased grazing pressure by this newly introduced species. For the period 1977-l 990, mean estimated primary production was only 39 g C mm2 yr-’ during years when bivalve suspension feeders were abundant (>2,000 mm2), compared to 106 g C m-2 yr-’ when bivalves were absent or present in low numbers. These observations support the hypothesis that seasonal and interannual fluctuations in estuarine phytoplankton biomass and primary production can be regulated jointly by direct physical effects (e.g. river-driven transport) and trophic interactions (episodes of enhanced grazing pressure by immigrant populations of benthic suspension feeders).

A flume system and protocol for measuring the filtration rate of infaunal bivalves is described. Assemblages of multi-sized clams, at natural densities and in normal filter-feeding positions, removed phytoplankton suspended in a unidirectional flow of water. The free-stream velocity and friction velocity of the flow, and bottom roughness height were similar to those in natural estuarine waters. Continuous variations in phytoplankton (Chroomonas salinay) cell density were used to measure the filtration rate of the suspension-feeding clam Potamocorbula amurensis for periods of 2 to 28 h. Filtration rates of P. amurensis varied from 100 to 580 liters (gd)-1 over a free-stream velocity range of 9 to 25 cm s-1. Phytoplankton loss rates were usually constant throughout the experiments. Our results suggest that suspension-feeding by infaunal bivalves is sensitive to flow velocity.

An assessment was made in Suisun Bay, California, of the distributions of hydrocarbons in estuarine bed and suspended sediments and in the recently introduced asian clam, Potamocorbula amurensis. Sediments and clams were contaminated with hydrocarbons derived from petrogenic and pyrogenic sources. Distributions of alkanes and of hopane and sterane biomarkers in sediments and clams were similar, indicating that petroleum hydrocarbons associated with sediments are bioavailable to Potamocorbula amurensis. Polycyclic aromatic hydrocarbons in the sediments and clams were derived mainly from combustion sources. Potamocorbula amurensis is therefore a useful bioindicator of hydrocarbon contamination, and may be used as a biomonitor of hydrocarbon pollution in San Francisco Bay.

Time courses for ingest~on, retention and release via feces of microbial food was investigated using 2 b~valves w ~ t h d~fferent feeding strategies, Potamocorbula amurensis and Macoma balthica. The results showed 2 pathways for the uptake of food material in these clams. The first is represented by an initlal label pulse in the feces. The second pathway operates over longer time periods. Inert "Cr-labeled beads were used to determine time frames for these pathways. The first pathway, involving extracellular digestion and intestinal uptake, is relatively inefficient In the digestion of bacter~al cells by P amurensis but more efficient in M. balthica. The second pathway, involving intracellular digestion withln the digestive gland of both clams, was highly efficient in absorb~ng bacterial carbon, and was responsible for most chromium uptake. Differences in the overall retention of microbial "Cr and I4C relate not to gut-passage times but to the processing and release strategies of the food material by these 2 clams.

For biomarkers to be useful in assessing anthropogenic impacts in field studies involving aquatic organisms, they should not be affected by naturally occurring changes in environmental parameters such as salinity. This is especially important in estuarine environments and for relatively unspecific biomarkers like heat-shock proteins (hsps, stress proteins). In this study, the heat-shock protein response was measured in the euryhaline clam, Potamocorbula amurensis, after exposure to a range of salinities reflecting normal and extreme environmental conditions in Northern San Francisco Bay, California. The ability to raise cellular hsp70 levels in response to heat-shock was significantly impaired in P. amurensis collected from a low (0.5 ppt) salinity field site, and after 14 day exposure to low salinity in the laboratory.

Bivalves are commonly used to detect metal pollution in the marine environment. Commercially cultured Milky oysters (Saccostrea commercialis) were transplanted in various sites along the North Queensland coast and analyzed for two metals of potentially anthropogenic origin (Cd, Zn). To provide additional information, naturally occurring Black Lip oysters (Saccostrea echinata) were also collected at the transplantation sites. The study demonstrated that the oysters species transplanted are good bioindicators of these metal concentrations in tropical waters, sensitive to variations in the environment at concentrations which are much smaller than pollution signals commonly reported for temperate waters. Three transplant experiments were carried out from May 1999 to February 2000. Milky oysters transplanted to offshore areas (Orpheus Is., Kelso Reef) accumulated Cd in the soft parts whereas oysters sampled from cages placed in Ross Creek and the Herbert River estuaries showed a decrease in Cd concentration, which resulted from an increase in dry weight. Dry weight appeared to be an important covariant affecting Cd concentration in the oysters whereas it does not unambiguously affect Zn concentrations. For the duration of the experiments, oysters sampled from the Magnetic Is. reference site showed effectively constant Cd concentrations and total Cd contents which indicates that any seasonal cycle affecting metal concentration is weak. It was found that Cd accumulation in oysters increased as ambient dissolved Cd concentration decreased, from which it was concluded that for these oysters, the predominant source of Cd was from the particulate phase rather than the dissolved phase.

Following the aggressive invasion of the bivalve, Potamocorbula amurensis, in the San Francisco Bay-Delta in 1986, selenium contamination in the benthic food web increased. Concentrations in this dominant (exotic) bivalve in North Bay were three times higher in 1995–1997 than in earlier studies, and 1990 concentrations in benthic predators (sturgeon and diving ducks) were also higher than in 1986. The contamination was widespread, varied seasonally and was greater in P. amurensis than in co-occurring and transplanted species. Selenium concentrations in the water column of the Bay were enriched relative to the Sacramento River but were not as high as observed in many contaminated aquatic environments. Total Se concentrations in the dissolved phase never exceeded 0.3 g Se per l in 1995 and 1996; Se concentrations on particulate material ranged from 0.5 to 2.0 g Se per g dry weight (dw) in the Bay. Nevertheless, concentrations in P. amurensis reached as high as 20 g Se per g dw in October 1996. The enriched concentrations in bivalves (6–20 g Se per g dw) were widespread throughout North San Francisco Bay in October 1995 and October 1996. Concentrations varied seasonally from 5 to 20 g Se per g dw, and were highest during the periods of lowest river inflows and lowest after extended high river inflows. Transplanted bivalves (oysters, mussels or clams) were not effective indicators of either the degree of Se contamination in P. amurensis or the seasonal increases in contamination in the resident benthos. Se is a potent environmental toxin that threatens higher trophic level species because of its reproductive toxicity and efficient food web transfer. Bivalves concentrate selenium effectively because they bioaccumulate the element strongly and lose it slowly; and they are a direct link in the exposure of predaceous benthivore species. Biological invasions of estuaries are increasing worldwide. Changes in ecological structure and function are well known in response to invasions. This study shows that changes in processes such as cycling and effects of contaminants can accompany such invasions. © 2002 Published by Elsevier Science B.V.

South San Francisco Bay, USA, is a shallow coastal embayment that receives large inputs of nutrients (N. P, Si) and small local inputs of freshwater. Phytoplankton dynamics are typically characterized by a spring bloom when surface chlorophyll a increases from 40 mg m-3. The bloom persists for 2 to 4 wk, and then dissipates. Phytoplankton biomass remains low (chlorophyll a < 5 mg m-3) from May through December, although light and nutrient availability are sufficient to sustain growth rates of 1 to 1.5 divisions d-' in the expansive shallows. Transport processes apparently exert a small influence on phytoplankton biomass, and calculated zooplankton grazing accounts for only a small reduction in net rate of phytoplankton population growth in the shallows. However, suspension-feeding bivalves are sufficiently abundant to filter a volume equivalent to the volume of South Bay at least once daily. These observations suggest that grazing by benthos is the primary mechanism controlling phytoplankton biomass during summer and fall.

Among the consequences of extremely low river flow into northern San Francisco Bay during a two-year drought were (1) a gradual increase in salinity, (2) an unusual decline in chlorophyll a concentration, and (3) the upstream migration of estuarine benthic invertebrates to the normally brackish area of the bay. Total abundance in the benthos at a shallow monitoring site increased from a normal 2000 to greater than 20 000 individuals m −2 during the summer of 1977, presumably in response to the increased salinity. Estimated filtration rates derived from equations in the literature for one of the species, the suspended-feeding bivalve Mya arenaria ranged from 1 to 4 m 3 m −2 day −1 during 1977 depending on abundance and mean size on sampling dates. Because water depth at this site is less than 2 m, Mya could have filtered all of the particles (including diatoms) from the water column on the order of once per day. Several other immigrant species undoubtedly contributed to the removal of particles from the near-bottom water as well. Increased benthic grazing, therefore, could have accounted for the anomalously low phytoplankton biomass observed during the drought. These results suggest that during periods of prolonged low river flow and increased salinity benthic food webs could become more important than planktonic food webs in the upper part of the estuary.

Abiotic factors and species introductions can alter food web timing, disrupt life cycles, and change life history expressions and the temporal scale of population dynamics in zooplankton communities. We examined physical, trophic, and zooplankton community dynamics in the San Francisco Estuary, California, a highly altered Mediterranean climate waterway, across a 43-year dataset (1972–2014). Before invasion by the suspension-feeding overbite clam (Potamocorbula amurensis) in the mid-1980s, the estuary demonstrated monomictic thermal mixing in which winter turbidity and cool temperatures contributed to seasonally low productivity, followed by a late-spring-summer clearing phase with warm water and peak phytoplankton blooms that continued into early winter. Following the clam invasion, we observed a shift in peak phytoplankton bloom timing, with peak productivity now occurring in May compared to June prior to the invasion. Peak abundance of several zooplankton taxa (Eurytemora affinis, Pseudodiaptomus, other calanoids, and non-copepods) also shifted to earlier in the season. We present the first evidence of a shift in the timing of peak abundance for zooplankton species that are key prey items of delta smelt (Hypomesus transpacificus), a federally threatened pelagic fish species. These timing shifts may have exacerbated well-documented food limitations of delta smelt due to declines in primary productivity since the invasion of the overbite clam. Future conservation efforts in the estuary should consider measures designed to restore the timing and magnitude of pre-invasion phytoplankton blooms.