Search

Invasive species exert disproportionate impacts in wetlands and pose particular challenges for rare species persisting at small spatial scales. In the urbanized San Francisco Estuary (SFE), which contains 90% of California's remaining coastal wetlands, invasive and rare species often co-occur. One narrow endemic taxon, the federally listed Suisun thistle (Cirsium hydrophilum var. hydrophilum) is restricted to two or three locations where the invasive perennial pepperweed (Lepidium latifolium) has an increasing presence. Perennial pepperweed has invaded salt, brackish, and freshwater wetlands around the SFE, leading to high management concern. In this study, we investigated how perennial pepperweed may contribute to further rarity of the Suisun thistle, by conducting a removal experiment and surveying soil-plant relationships. Removing pepperweed led to a doubling of native species relative cover and an increase in native species richness by an average of one species per plot, positive effects on Suisun thistle cover, number, and reproductive output, and shifts in soil properties. Combined with survey data inside and outside of pepperweed stands, we conclude that pepperweed competes with Suisun thistle via competition for space, nutrients, and light, interferes with the Suisun thistle's reproductive success, and alters brackish marsh soil physicochemical characteristics to further favor pepperweed. We recommend local control of pepperweed to prevent further loss of Suisun thistle. Further, the wide range of mechanisms by which this invasion may proceed if unchecked should be considered in other settings where rare or uncommon species are at risk from invaders. [ABSTRACT FROM AUTHOR]

Drivers of phytoplankton and zooplankton dynamics vary spatially and temporally in estuaries due to variation in hydrodynamic exchange and residence time, complicating efforts to understand controls on food web productivity. We conducted approximately monthly (2012–2019; n = 74) longitudinal sampling at 10 fixed stations along a freshwater tidal terminal channel in the San Francisco Estuary, California, characterized by seaward to landward gradients in water residence time, turbidity, nutrient concentrations, and plankton community composition. We used multivariate autoregressive state space (MARSS) models to quantify environmental (abiotic) and biotic controls on phytoplankton and mesozooplankton biomass. The importance of specific abiotic drivers (e.g., water temperature, turbidity, nutrients) and trophic interactions differed significantly among hydrodynamic exchange zones with different mean residence times. Abiotic drivers explained more variation in phytoplankton and zooplankton dynamics than a model including only trophic interactions, but individual phytoplankton–zooplankton interactions explained more variation than individual abiotic drivers. Interactions between zooplankton and phytoplankton were strongest in landward reaches with the longest residence times and the highest zooplankton biomass. Interactions between cryptophytes and both copepods and cladocerans were stronger than interactions between bacillariophytes (diatoms) and zooplankton taxa, despite contributing less biovolume in all but the most landward reaches. Our results demonstrate that trophic interactions and their relative strengths vary in a hydrodynamic context, contributing to food web heterogeneity within estuaries at spatial scales smaller than the freshwater to marine transition. [ABSTRACT FROM AUTHOR]

There is much debate about the extent to which water management in the upper San Francisco Estuary, California, affects the habitat and status of delta smelt (Hypomesus transpacificus), an endemic fish protected under the US and California Endangered Species Acts. For example, current management reflects the hypothesis that salinity, and in some cases the location of the tidally averaged salinity of 2 parts per thousand (X2), is a reliable indication of habitat quality. We evaluated hypotheses about environmental drivers of the quality of delta smelt habitat (probability of occupancy) during autumn that were developed by experts on the species and estuary. We fit Bayesian occupancy models, which account for imperfect detection, and identified those that best predicted the presence of delta smelt in catch data from 1980 to 2015. The most strongly supported model indicated that occupancy was associated with salinity (measured as specific conductance) and temperature, and detection was associated with body size, sample volume, water clarity, and tidal stage. The second most strongly supported model indicated that occupancy was associated with the abundance of a hypothesized competitor, threadfin shad (Dorosoma petenense), an expert-elicited index of predation intensity, and water clarity, and detection was associated with body size, sample volume, water clarity, and time of day. Our results suggested that clarity did not affect occupancy, but affected finer-resolution processes of local presence and detection at sampling stations. Spatial patterns in occupancy were consistent in wet and dry years, suggesting that management on the basis of salinity oversimplifies estimation of habitat quantity and quality. [ABSTRACT FROM AUTHOR]

Variation in freshwater flow into estuaries can profoundly alter abundance of estuarine organisms through a variety of mechanisms. In the San Francisco Estuary, California, an annual abundance index of juvenile longfin smelt Spirinchus thaleichthys has varied by ~ 100-fold over the range of flow, and over the last five decades the index has declined by over 100-fold. The unknown mechanisms for variation with flow may include removal of larvae by freshwater diversions during low-flow periods. Using data from larval trawl surveys during January–March 2009–2020, we estimated larval population size, its response to freshwater flow, and losses of larvae to freshwater diversions. Population size was estimated by a Bayesian hierarchical model linking a process model, with salinity and water clarity as covariates, to an observation model representing catch by a negative binomial distribution. Population size averaged across surveys within years—an index of the number of larvae produced—decreased over the study period from ~ 109 to 108 larvae. Population size was unrelated to freshwater flow in the year of hatching but positively related to the subsequent juvenile abundance index. Thus, the mechanisms underlying the strong variability in the annual abundance index of longfin smelt with freshwater flow are constrained to occur after March. Estimated proportional losses to water diversions accumulated over the period of vulnerability averaged 1.5% of the population, too low to measurably influence population dynamics. [ABSTRACT FROM AUTHOR]

Estuarine food webs are fueled by multiple different primary producers. However, identifying the relative importance of each producer to consumers is difficult, particularly for fishes that utilize multiple food sources due to both their mobility and their generally high trophic levels. Previous studies have documented broad spatial differences in the importance of primary producers to fishes within the Upper San Francisco Estuary, California, including separation between pelagic and littoral food webs. In this study, we evaluated the importance of primary producers to adult fishes in three closely spaced subregions that represented disparate habitat types (a tidal wetland channel, a turbid backwater channel, and a deep open-water channel), each a potential outcome of local restoration projects. Using stable isotope analysis coupled with a Bayesian mixing model, we identified significant differences in primary-producer contribution to fishes and invertebrates across habitats and seasons, especially in the relative contribution of submersed aquatic vegetation and phytoplankton. Most fishes utilized multiple primary producers and showed little segregation between pelagic and littoral food webs among habitats. Availability of primary producers differs seasonally and across multiple spatial scales, helping to buffer environmental variability and thus enhancing food web resilience. Ecosystem restoration may improve with emphasis on restoring a wide variety of primary producers to support consumers. [ABSTRACT FROM AUTHOR]

Two threatened osmerid species native to the San Francisco Estuary (SFE)—Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys)—are subject to broad human influence, including significant habitat alteration and the presence of the introduced osmerid, Wakasagi (Hypomesus nipponensis). The identification of these closely related species and their hybrids is difficult in field collected specimens which are subject to damage through handling and may be difficult to identify morphologically, especially when young. In addition, it is known that these three species hybridize, but the extent and effect of hybridization is difficult to quantify and monitor. We developed assays for 24 species-specific single nucleotide polymorphisms (SNPs) that identify whether a sample is a pure species (Delta Smelt, Longfin Smelt, or Wakasagi), a first generation (F1) hybrid, or a backcross. We used this SNP panel to genetically identify wild osmerids collected in Yolo Bypass from 2010 to 2016 and detected nine Delta Smelt × Wakasagi F1 hybrids and two Wakasagi × (Delta Smelt × Wakasagi) backcross hybrids; all assayed hybrids had Wakasagi as the maternal parent. The backcrossing into Wakasagi suggests that hybridization may only occur in one direction and thus preclude introgression to Delta Smelt. We also found substantial morphological field misidentifications (32.7%) in the Yolo Bypass samples resulting in more Wakasagi and fewer Delta Smelt than previously recorded when based on morphology. The SNP panel described in this study constitutes a valuable resource for monitoring hybridization in the SFE and assigning species identifications with accuracy and efficiency. [ABSTRACT FROM AUTHOR]

The southern-most reproducing Longfin Smelt population occurs in the San Francisco Estuary, California, USA. Long-term monitoring of estuarine habitat for this species has generally only considered deep channels, with little known of the role shallow waters play in supporting their early life stage. To address the need for focused research on shallow-water habitat, a targeted study of Longfin Smelt larvae in littoral habitat was conducted to identify potential rearing habitats during 2013 and 2014. Our study objectives were to (1) determine if larval densities vary between littoral habitats (tidal slough vs. open-water shoal), (2) determine how larval densities in littoral habitats vary with physicochemical and biological attributes, (3) determine if larval densities vary between littoral habitats and long-term monitoring channel collections, and (4) determine what factors predict larval rearing distributions from the long-term monitoring channel collections. Larval densities did not vary between littoral habitats but they did vary between years. Water temperature, salinity, and chlorophyll a were found important in predicting larval densities in littoral habitats. Larval densities do not vary between littoral and channel surveys; however, the analysis based on channel data suggests that Longfin Smelt are hatching and rearing in a much broader region and under higher salinities (∼2-12 psu) than previously recognized. Results of this study indicate that conservation efforts should consider how freshwater flow, habitat, climate, and food webs interact as mechanisms that influence Longfin Smelt recruitment in estuarine environments. [ABSTRACT FROM AUTHOR]

Anthropogenic changes have dramatically transformed the upper San Francisco Estuary over the past two centuries. Key changes influencing the region’s hydrology and hydrodynamics include land use changes, levee construction and channel modifications, upstream reservoir construction, and out-of-basin water exports. In order to examine how these changes have altered the physical characteristics of the estuary, 3-D hydrodynamic models were constructed to study the system in its “pre-development” condition, prior to significant modern anthropogenic influence, and in its contemporary condition. The pre-development system model was calibrated by varying marsh plain elevations in order to match sparse observations of tidal characteristics; the contemporary system model was calibrated to observed flow, stage, and salinity data. A recent three-year period covering a wide range of flow conditions was used to compare and contrast the hydrodynamic behavior of the two systems. While the contemporary model simulation assumed historical observed boundary conditions, the pre-development model simulation assumed conditions thought to exist prior to the alterations of the past two centuries. The relationship between estuary outflow and the longitudinal distance from the estuary mouth to the 2 psu bottom salinity isohaline (X2) was analyzed. Salt intrusion in the pre-development system was found to be slightly more sensitive to outflow and responded faster to changes in outflow than in the contemporary system. Changes in estuary outflows were responsible for more of the salt intrusion differences between the two systems than were changes in estuary geometry and bathymetry. An analysis of the physical mechanisms contributing to salt intrusion found tidal trapping and other unsteady processes to be more important in the pre-development estuary than in the contemporary one. In both systems, steady processes such as estuarine circulation were strongest during neap tides and unsteady salt intrusion processes were strongest during spring tides, resulting in limited spring-neap variability in salt intrusion. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Using stable isotopes of carbon (δ13C) and nitrogen (δ15N) and mixing models, we investigated the trophic levels and carbon sources of invertebrates and fishes of a large tidal marsh in the San Francisco Estuary. Our goal was to better understand an estuarine food web comprised of native and alien species. We found the following: (1) the food web was based largely on carbon from phytoplankton and emergent-aquatic and terrestrial vegetation, but carbon from submerged aquatic vegetation and phytobenthos was also used; (2) alien species increased the complexity of the food web by altering carbon-flow pathways and by occupying trophic positions different from native species; and (3) most consumers were dietary generalists. [ABSTRACT FROM AUTHOR]

Abstract: Anthropogenic activities in watersheds can have profound effects on sediment transport through river systems to estuaries. Disturbance in a watershed combined with alterations to the hydro-climatologic regime may result in changes to the sediment flux, and exacerbate the impacts of extreme events (such as large-magnitude floods) on sediment transport. In the San Francisco Estuary, suspended sediment has been declining over the past 30years as a result of declining sediment supply, contributing to dramatic changes in the ecology and geomorphology of the estuary. However, the decline has not been gradual. Recent observations of an abrupt decrease in suspended sediments in the San Francisco Bay have been explained by a model that suggests that the step change has occurred due to exceedance of a sediment regulation threshold that triggered the change from a sediment transport regime to a supply-limited system. We investigated structural changes in the historical record of total suspended solids (TSS) concentration measured in the upper estuary to verify the model predictions. TSS in the upper estuary exhibited an abrupt step decrease in 1983 corresponding to the record-high winter and summer flows from the 1982 to 1983 El Niño event. After this step change, TSS concentrations had a significant declining trend despite subsequent near-record high flows. The abrupt change in TSS followed by the declining trend provides evidence for the hypothesis of sediment supply limitation in the San Francisco Estuary. [Copyright &y& Elsevier]

Abstract: While bone stable isotope signatures of humans foraging in open coastal and fully terrestrial environments have been relatively well documented, the signature of foraging near brackish-water estuaries is less well known. This study examines the Central California isotopic landscape, or isoscape, showing how foods in different ecosystems have distinctive isotopic compositions. We present new bone collagen and apatite stable isotope data from two Late Holocene sites (CA-SOL-11 and CA-SOL-69) near Suisun Marsh, a low salinity brackish water estuary upstream from San Francisco Bay. Faunal remains at the sites include significant numbers of aquatic resources including fish and shellfish, in addition to terrestrial mammals, while paleobotanical remains suggest mainly terrestrial nuts and seeds. Stable isotope data at the population level corroborate this finding and show consumption of significant levels of brackish water nutrients, including both dietary protein and dietary carbohydrates and fats, paired with terrestrial foods. This dietary focus generates a unique brackish-water isotopic signature that is distinct from others in Central California. The documentation of an isoscape with strong regional gradients can be of tremendous help in reconstructing ancient patterns in subsistence, migration, and trade. [Copyright &y& Elsevier]

The release of hatchery reared salmonid smolts is a common management tool aimed at enhancing depleted wild stocks and maintaining fisheries throughout Northern California and the Pacific Northwest. In the Sacramento River watershed, smolts must migrate through the river, delta and estuary in order to successfully reach the Pacific Ocean. Migration success (success defined as apparent survival from one monitor location to another) may vary between species, year and habitat. We released 500 late-fall run Chinook salmon and 500 steelhead smolts in 2009 and 2010 in the Sacramento River (river kilometer 207). Each smolt was implanted with a coded ultrasonic tag, which was detected by an array of over 300 underwater receiver stations deployed throughout the system. Less than 25 % of fish migrated successfully to the Pacific Ocean in both years. We found that reach specific success was greater in the Delta in 2009 (>60 %) than in 2010 (<33 %), whereas this pattern was reversed in the Bay (<57 % in 2009, >75 % in 2010). Identifying the location, timing and causes of smolt mortality can lead to improved management of the resource. [ABSTRACT FROM AUTHOR]

We measured primary production during spring-summer 2006-2007 to determine the carbon supply to the low-salinity pelagic food web of the San Francisco Estuary (SFE). Weekly or biweekly samples were taken at three stations of fixed salinity for size-fractionated primary production and biomass, both as chlorophyll and from biovolume based on counts. Error variance in productivity estimates arose mainly from the depth integration of C uptake, showing the importance of productivity measurements at high light levels for estimates of depth-integrated production. Temporal and spatial variability in production were surprisingly small. Combining data from this study with long-term monitoring data, productivity and biomass were variable in time and salinity but without persistent patterns and with infrequent blooms. Production within the low-salinity zone was unresponsive to variation in freshwater flow, in contrast to findings in other estuaries where nutrient loading drives variability in production and other regions of the SFE where production responds to residence time or to stratification. Estimated annual primary production was only 25 and 31 g C m year during 2006 and 2007, only half of it in cells >5 μm. These results imply that phytoplankton provided poor food web support for higher trophic levels, probably contributing to the long-term decline in fish abundance in the brackish to freshwater region of the estuary. [ABSTRACT FROM AUTHOR]

Depth-integrated primary production (Σ P, in grams of carbon per square meter per day) was measured using C in the northern San Francisco Estuary (SFE) from March through August of 2006 and 2007. Determinations of Σ P were then used to calibrate a published light-utilization model that relates Σ P to a composite parameter of chlorophyll, solar irradiance, and photic zone depth. The resultant calibration coefficient, Ψ, varied by a factor of nearly two between 2006 and 2007 and was lower than determined in previous calibrations for the estuary. The now chronically low chlorophyll concentrations in the SFE have resulted in lower predictive power of the light-utilization model. The variation in Ψ was likely the result of interannual variation in phytoplankton assimilation number. These results suggest that using a single Ψ may yield large errors in estimated estuarine production when applied overbroad spatial and temporal scales. Given the food-limited condition of the SFE, it appears that direct measurements of primary production are necessary for accurately characterizing the base of the estuarine food web. [ABSTRACT FROM AUTHOR]

Abstract: We describe the results of a series of 96-h enclosure experiments conducted using water from stations in the northern San Francisco Estuary (SFE) along a gradient in ammonium (NH4) and nitrate (NO3) concentrations. Using dual-labeled 13C/15N tracers, we followed the timing and sequence of primary (carbon, C) production and phytoplankton nitrogen (N) use during experimental phytoplankton blooms. Our results show that diatoms consistently drive the phytoplankton blooms in the enclosures. By tracing both C and N uptake we provide clear evidence that high rates of C uptake are linked to phytoplankton NO3, and not NH4, use. Results from kinetics experiments demonstrated higher specific uptake rates (VMAx) for NO3 compared to NH4 in the SFE. Finally, dissolved inorganic carbon and nutrient drawdown ratios in the enclosures from the chronically high NH4 regions of the SFE were substantially lower than predicted from the Redfield ratio, suggesting suppressed C uptake, in relation to other elemental uptake. Our conceptual model of the DIN interactions that lead to higher primary production and phytoplankton blooms in the SFE suggests that higher rates of primary production that accompany phytoplankton NO3 uptake are sufficient to outpace phytoplankton losses, leading to blooms, compared to the lower rates associated with NH4 uptake (only 20% of that based upon NO3). Historical changes in wastewater practices have increased the proportion of NH4 to the DIN pool in the SFE leading to reduced access to NO3 by phytoplankton. This may help to explain some of the reduced primary production and phytoplankton biomass observed there since the 1970s. [Copyright &y& Elsevier]

Abstract: Primary production in the Northern San Francisco Estuary (SFE) has been declining despite heavy loading of anthropogenic nutrients. The inorganic nitrogen (N) loading comes primarily from municipal wastewater treatment plant (WTP) discharge as ammonium (NH4). This study investigated the consequences for river and estuarine phytoplankton of the daily discharge of 15 metric tons NH4–N into the Sacramento River that feeds the SFE. Consistent patterns of nutrients and phytoplankton responses were observed during two 150-km transects made in spring 2009. Phytoplankton N productivity shifted from NO3 use upstream of the WTP to productivity based entirely upon NH4 downstream. Phytoplankton NH4 uptake declined downstream of the WTP as NH4 concentrations increased, suggesting NH4 inhibition. The reduced total N uptake downstream of the WTP was accompanied by a 60% decline in primary production. These findings indicate that increased anthropogenic NH4 may decrease estuarine primary production and increase export of NH4 to the coastal ocean. [Copyright &y& Elsevier]

Abstract: Benthic indices to support aquatic environmental condition assessments have been more effectively developed for higher than lower salinity habitats. Here we quantify agreement among benthic experts using best professional judgment to assess community condition of mesohaline and tidal freshwater samples from the San Francisco Estuary and Delta, and compare that to a previous study for San Francisco Estuary polyhaline samples. Benthic species abundance data from 20 sites in each habitat were provided to 7 tidal freshwater, and 8 mesohaline, experts who ranked the samples from best to worst condition and placed the samples into 4 condition categories. The average correlation among expert''s condition rankings was only 0.38 and 0.29 in the mesohaline and tidal freshwater habitats, respectively, compared to 0.92 in the previous polyhaline study. Pair-wise agreement among expert condition categories averaged 41% and 39%, compared to 70% in the polyhaline. Based on post-exercise discussions among the experts, the differences in agreement among habitats appears related to the use of different indicator taxa and to disturbance regimes in the lower salinity habitats that select for higher proportions of tolerant taxa, confounding assessments at the current level of understanding of benthic response in these habitats. Regardless of the reason, the absence of a clear conceptual model and agreement among benthic ecologists about benthic condition makes index development more difficult in low salinity estuarine and tidal freshwater habitats. [Copyright &y& Elsevier]

Decline of native pelagic species in estuarine systems is an increasing problem, especially for native fishes in the San Francisco Estuary and Delta (SFE-D). Addressing these losses depends on understanding trophodynamics in the food web that supports threatened species. We quantified the role of microzooplankton (heterotrophic-mixotrophic protists <200 μm) in the food web of the upper SFE-D. We sampled protist plankton abundance and composition at two sites (Suisun Bay and Grizzly Bay) approximately monthly from February 2004 to August 2005 and conducted dilution experiments during spring and summer of both years in Suisun Bay. Heterotrophs dominated the protist community in Suisun Bay and Grizzly Bay, particularly in the <20 μm size range, and peaks in protistan microzooplankton biomass were associated with high phytoplankton biomass. In both years, microzooplankton grazing rates were high (0.5-0.7 day) during the spring and lower (~0.2 day) during summer. Phytoplankton growth rates peaked in April 2004 (~0.7 day) but were much lower (<0.1 day) in spring 2005, despite relatively high abundance. Thus, microzooplankton grazing consumed as much as 73% of phytoplankton standing stock during spring and ~15% of standing stock during summer of both years. Combined with earlier results, we conclude that microzooplankton can be important mediators of carbon and energy flow in the upper SFE-D and may be a 'source' to the metazoan food web. [ABSTRACT FROM AUTHOR]

BSTRACT [ABSTRACT FROM AUTHOR]

Future development and climate change pose potentially serious threats to estuarine fish populations around the world. We examined how habitat suitability for delta smelt ( Hypomesus transpacificus), a state and federally protected species, might be affected by changes in outflow in the San Francisco Estuary due to future development and climate change. Forty years of sampling data collected during fall from 1967 to 2008 were examined to define abiotic habitat suitability for delta smelt as a function of salinity and water transparency, and to describe long-term trends in habitat conditions. The annual habitat index we developed, which incorporated both quantity and quality of habitat, decreased by 78% over the study period. Future habitat index values under seven different development and climate change scenarios, representing a range of drier and wetter possibilities, were predicted using a model which related estuarine outflow to the habitat index. The results suggested that each of the scenarios would generally lead to further declines in delta smelt habitat across all water year types. Recovery targets for delta smelt will be difficult to attain if the modeled habitat conditions are realized. [ABSTRACT FROM AUTHOR]

1. Increasing blooms of Microcystis aeruginosa have unknown impacts on the copepods Eurytemora affinis and Pseudodiaptomus forbesi, which are the dominant zooplankters and key prey species for endangered larval fish in the upper San Francisco Estuary. 2. Laboratory feeding experiments were designed to measure the effect of Microcystis on copepod survival and to distinguish the effects of toxicity and nutrition. In a series of survival tests, copepods were fed a mixed diet of algae plus one of two strains of Microcystis, either producing (MC+) or lacking microcystin (MC−). 3. Microcystis significantly reduced survival even when it was a small proportion of the diet, indicating that toxicity was the major cause of mortality. Contrary to expectation, however, the MC+ strain did not result in higher mortality, suggesting that non-MC metabolites of Microcystis can be toxic to copepods. 4. Across treatments, survival of P. forbesi was greater than that of E. affinis, although the two copepods responded differently to both the ratio and the strain of Microcystis in their food. Survival of P. forbesi was greater on the MC+ strain and was inversely proportional to the ratio of dietary Microcystis (MC+ or MC−). In contrast, survival of E. affinis declined similarly across treatments and was not related to the proportion or strain of dietary Microcystis. Results indicate that the copepod P. forbesi can coexist with Microcystis while the other copepod E. affinis cannot. 5. Regardless of species, dietary Microcystis caused significant mortality to copepods, and it may cause adverse impacts to the potentially food-limited zooplankton community of the San Francisco Estuary. These impacts may not be related to the cellular MC concentration because Microcystis contains other metabolites that negatively affect copepods. [ABSTRACT FROM AUTHOR]

Total mercury (Hg) concentrations were determined in fillet tissue of sport fish captured in the Sacramento–San Joaquin River Delta and surrounding tributaries, a region particularly impacted by historic gold and mercury mining activity. In 1999 and 2000, mercury concentrations were measured in 767 samples from ten fish species. Largemouth bass (Micropterus salmoides), the primary target species, exhibited a median Hg concentration of 0.53 μg g−1 (N =406). Only 23 largemouth bass (6%) were below a 0.12 μg g−1 threshold corresponding to a 4 meals per month safe consumption limit. Most of the largemouth bass (222 fish, or 55% of the sample) were above a 0.47 μg g−1 threshold corresponding to a 1 meal per month consumption limit. Striped bass (Morone saxatilis), channel catfish (Ictalurus punctatus), white catfish (Ameirus catus), and Sacramento pikeminnow (Ptychocheilus grandis) also had relatively high concentrations, with 31% or more of samples above 0.47 μg g−1. Concentrations were lowest in redear (Lepomis microlophus) and bluegill (Lepomis macrochirus) sunfish, with most samples below 0.12 μg g−1, suggesting that targeting these species for sport and subsistence fishing may reduce human dietary exposure to Hg in the region. An improved method of analysis of covariance was performed to evaluate spatial variation in Hg in largemouth bass captured in 2000, while accounting for variability in fish length. Using this approach, Hg concentrations were significantly elevated in the Feather River, northern Delta, lower Cosumnes River, and San Joaquin River regions. In spite of elevated Hg concentrations on all of its tributaries, the central Delta had concentrations that were low both in comparison to safe consumption guidelines and to other locations. [Copyright &y& Elsevier]

Where tributaries meet, certain conditions of flow and topography often result in incomplete mixing and the formation of spatially and temporally persistent plumes or bands. Yolo Bypass, the primary floodplain of the lower Sacramento River (California, USA), provides an extreme example of this effect. Inspection of recent and historical aerial photographs revealed that the four major tributaries of Yolo Bypass typically do not substantially mix laterally within the floodplain. The phenomenon is notable in the number of tributaries involved (4), the distance over which the bands remain distinct (>61 km), and the persistence of the bands despite channel constrictions and long cross-wind fetch. This effect demonstrates the importance of lateral variability during floodplain flow events, including transport and distribution of chemical constituents, and habitat for fish and other organisms that use floodplains as migration corridors and rearing areas. [ABSTRACT FROM AUTHOR]

Abstract: Concentrations of many anthropogenic contaminants in the San Francisco Estuary exist at levels that have been associated with biological effects elsewhere, so there is a potential for them to cause biological effects in the Estuary. The purpose of this paper is to summarize information about biological effects on the Estuary''s plankton, benthos, fish, birds, and mammals, gathered since the early 1990s, focusing on key accomplishments. These studies have been conducted at all levels of biological organization (sub-cellular through communities), but have included only a small fraction of the organisms and contaminants of concern in the region. The studies summarized provide a body of evidence that some contaminants are causing biological impacts in some biological resources in the Estuary. However, no general patterns of effects were apparent in space and time, and no single contaminant was consistently related to effects among the biota considered. These conclusions reflect the difficulty in demonstrating biological effects due specifically to contamination because there is a wide range of sensitivity to contaminants among the Estuary''s many organisms. Additionally, the spatial and temporal distribution of contamination in the Estuary is highly variable, and levels of contamination covary with other environmental factors, such as freshwater inflow or sediment-type. Federal and State regulatory agencies desire to develop biological criteria to protect the Estuary''s biological resources. Future studies of biological effects in San Francisco Estuary should focus on the development of meaningful indicators of biological effects, and on key organism and contaminants of concern in long-term, multifaceted studies that include laboratory and field experiments to determine cause and effect to adequately inform management and regulatory decisions. [Copyright &y& Elsevier]

Abstract: Sediment age profiles reconstructed from a sequence of historical bathymetry changes are used to investigate the subsurface distribution of historical sediments in a subembayment of the San Francisco Estuary. Profiles are created in a grid-based GIS modeling program that stratifies historical deposition into temporal horizons. The model''s reconstructions are supported by comparisons to profiles of 137Cs and excess 210Pb at 12 core sites. The predicted depth of the 1951 sediment horizon is positively correlated to the depth of the first occurrence of 137Cs at sites that have been depositional between recent surveys. Reconstructions at sites that have been erosional since the 1951 survey are supported by a lack of detectable 137Cs and excess 210Pb below the upper 6–16cm of the core. A new data set of predicted near-surface sediment ages was created to illustrate an application of this approach. Results demonstrate other potential applications such as guiding the spatial positioning of future core sites for contaminant measurements. [Copyright &y& Elsevier]

Habitat quality was assessed for two native osmerids, delta smelt Hypomesus transpacificus and longfin smelt Spirinchus thaleichthys, between two distinct nursery areas located in the low-salinity zone of the San Francisco estuary. The relationship between several variables was investigated including fish density, fish size, feeding success and the general condition of larvae as well as juveniles for both species. The nursery habitats that were evaluated included the North and South Channels of Suisun Bay. The results showed higher densities of zooplankton and decreased water velocities for the North Channel when compared to the South Channel. The dominant prey item was calanoid copepod Pseudodiaptomus forbesi for both species although longfin smelt residing in the North Channel also included another copepod in their diets, Acanthocyclops spp. In both locations, delta smelt fed predominantly during daytime flood tides, while longfin smelt feeding appeared to continue into the night hours. When both locations were compared, delta smelt in the North Channel exhibited higher densities, larger sizes, increased somatic condition and larvae <15 mm standard length demonstrated greater feeding success. Longfin smelt, exhibited similar densities, feeding success and size distributions between both channels, but generally showed poorer somatic condition for the South Channel, potentially due to energetic costs associated with documented vertical migration behaviour. Overall, the physical conditions of the North Channel provided superior habitat for both species, while the South Channel afforded only marginal habitat for longfin smelt and very poor habitat for delta smelt. Therefore, the North Channel of Suisun Bay acts as critical nursery habitat by providing better feeding and growing conditions leading to increased health and survival for both species. [ABSTRACT FROM AUTHOR]

Estuaries are dynamic environments at the land-sea interface that are strongly affected by interannual climate variability. Ocean-atmosphere processes propagate into estuaries from the sea, and atmospheric processes over land propagate into estuaries from watersheds. We examined the effects of these two separate climate-driven processes on pelagic and demersal fish community structure along the salinity gradient in the San Francisco Estuary, California, USA. A 33-year data set (1980-2012) on pelagic and demersal fishes spanning the freshwater to marine regions of the estuary suggested the existence of five estuarine salinity fish guilds: limnetic (salinity = 0-1), oligohaline (salinity = 1-12), mesohaline (salinity = 6-19), polyhaline (salinity = 19-28), and euhaline (salinity = 29-32). Climatic effects propagating from the adjacent Pacific Ocean, indexed by the North Pacific Gyre Oscillation (NPGO), affected demersal and pelagic fish community structure in the euhaline and polyhaline guilds. Climatic effects propagating over land, indexed as freshwater outflow from the watershed (OUT), affected demersal and pelagic fish community structure in the oligohaline, mesohaline, polyhaline, and euhaline guilds. The effects of OUT propagated further down the estuary salinity gradient than the effects of NPGO that propagated up the estuary salinity gradient, exemplifying the role of variable freshwater outflow as an important driver of biotic communities in river-dominated estuaries. These results illustrate how unique sources of climate variability interact to drive biotic communities and, therefore, that climate change is likely to be an important driver in shaping the future trajectory of biotic communities in estuaries and other transitional habitats., (Published 2015. This article is a U.S. Government work and is in the public domain in the USA.)