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Broad infestations of invasive, non-native vegetation have transformed wetlands around the world. Ludwigia hexapetala is a widespread, amphibious invasive plant with a creeping growth habit in open water and an erect growth habit in terrestrial habitats. In the upper San Francisco Estuary of California, L. hexapetala is increasingly terrestrializing into marshes and this expansion may be facilitated by allelopathy. We conducted the first field-based study on L. hexapetala allelopathy to determine whether (1) three allelochemicals known to be exuded by L. hexapetala are expressed in situ, (2) the allelochemicals are detectable in leaves, soil, and water, and (3) allelopathic expression varies by season, salinity, and growth habit (open water "patch" vs. terrestrial marsh "interface" locations). Water, soil, and L. hexapetala leaves were collected in two freshwater sites and two oligohaline sites in the upper San Francisco Estuary in summer 2021, fall 2021, and spring 2022. Myricitrin and quercitrin, known allelochemicals, and salipurposid, a newly identified polyphenol, were detected in water, soil, and leaves. There were significant differences in allelochemical concentrations under fresh versus oligohaline conditions in water and soil, but not leaves. All three allelochemicals generally had higher concentrations in patch versus interface locations, suggesting that L. hexapetala allelopathy plays a greater competitive role in open water than terrestrial habitats. Leaf concentrations of each allelochemical varied seasonally; however, both myricitrin and salipurposid had heightened concentrations in spring. These results suggest that herbicide application in early spring may be most effective in controlling L. hexapetala terrestrialization from open water to marshes. [ABSTRACT FROM AUTHOR]

Objective: Delta Smelt Hypomesus transpacificus are thought to be close to extinction in the wild, which has spurred multiagency conservation efforts to supplement their population. In conjunction with these recent efforts, monitoring is needed to assess the effectiveness of supplementation. Such monitoring often uses large‐scale tagging of released fish to distinguish between hatchery‐origin and wild‐origin fish that are captured during later surveys. Methods: In this study, we evaluated the use of visible implant elastomer tags in Delta Smelt to determine whether fish survival, fish growth, or tag retention were dependent on (1) tag color (blue, green, orange, red, yellow, and no‐tag control) or (2) tagged body location (posterior‐dorsal, anterior‐dorsal, mid‐lateral line, and no‐tag control). Result: Over 165 days of the first experiment, there was no difference in growth rate (mean = 0.073 mm/d, range = 0.072–0.075 mm/d) or survival (mean = 68%, range = 63–77%) among tag colors. Across all color groups, mean tag retention was 96% (range = 87–100%). Over 120 days of the second experiment, tag location had no influence on fish growth rate (mean = 0.064 mm/d, range = 0.062–0.067 mm/d) or survival (mean = 50%, range = 43–58%). For the surviving fish in experiment 2, the tags that were placed at the mid‐lateral line were retained less (84% on day 120) than those at posterior‐dorsal and anterior‐dorsal locations (99% and 98%, respectively). Conclusion: Our results suggest that visible implant elastomer tagging is a suitable method for marking adult Delta Smelt (>50 mm fork length) for up to 165 days and can be useful for conservation monitoring efforts. Impact StatementSupplementation of Delta Smelt is needed to avert its extinction in the wild. We experimentally evaluated the suitability of visible implant elastomer tags to distinguish hatchery‐ and wild‐origin Delta Smelt captured in monitoring surveys during the spawning season. [ABSTRACT FROM AUTHOR]

Nutrient concentrations in many estuaries have increased over the past century due to increases in wastewater discharge and increased agricultural intensity, contributing to multiple environmental problems. Numerous biogeochemical and physical processes in estuaries influence nutrient concentrations during transport, resulting in complex spatial and temporal variability and challenges identifying predominant processes and their rates. Mechanistic models which require these rates to quantify biogeochemical processes become complex and difficult to calibrate as the number of processes and parameters grows, owing to the high dimensionality of the parameter space and the computational cost of simultaneously modeling the transport and transformations of constituents. We developed a modeling approach that decouples transport from transformations, enabling fast, data-driven exploration of the parameter space. The approach extracted information including water age, cumulative exposure to specific habitats, and mean water depth exposure from a hydrodynamic model. Using this information, a biogeochemical model was implemented to predict ammonium and nitrate concentrations in a Lagrangian frame. The model performed each simulation in milliseconds on a laptop computer, allowing the fitting of rate parameters for key transformations by optimization. The optimization used fixed station nitrate observations and the model was then validated against high-resolution mapping observations of ammonium and nitrate. The results suggest that the observed spatial and temporal variation can be largely represented with five transformation processes and their associated rates. Dissolved inorganic nitrogen (DIN) losses occurred only in shallow vegetated areas in the model, highlighting that biogeochemical processes in these areas should be included in DIN models. [ABSTRACT FROM AUTHOR]

Fishery independent monitoring in the San Francisco Estuary (SFE) includes extensive coverage by the many trawl- and seine-based surveys of the Interagency Ecological Program (IEP). These surveys primarily sample small forage fishes and/or juvenile life stages of larger fishes due to the relatively small net dimensions, mesh sizes, and tow speeds. As a result, the adult life stage of many SFE fish species is not completely sampled, representing a shortcoming in our ability to track changes in age-structured regional fish assemblages. To help fill this monitoring gap, we conducted an experimental gillnetting effort in the spring of 2023. We employed American Fisheries Society experimental gillnets in a stratified random sampling design in the North Delta, California, USA. In total, we caught 16 fish species during 141 approximately one-hour gillnet sets, including 33 paired day and night sets to test diurnal effects on catch. On average, fishes caught in this study were substantially larger than those caught by trawl- and seine-based surveys. Ordination analyses revealed a high degree of overlap in sampled fish assemblages between the three North Delta subregions (Cache Slough Complex, Lindsey Slough Complex, Liberty Slough Complex), with significant differences detected for only the Lindsey Slough Complex. When testing diel effects on catch, significant differences in species assemblage were seen between day and night sets. However, differences in catch may not justify the added risk and complexities of night sampling except for targeted studies of benthic predators (catfishes). Finally, while over 3,000 PIT tags were deployed (primarily in Striped Bass) between this and another nearby study, only 6 PIT tags were recovered, demonstrating that greater effort or different methodologies would be required to generate mark-recapture abundance estimates in this open and highly dynamic system. This study demonstrates the efficacy of experimental gillnets in sampling the large fish community within portions of the SFE and may inform future SFE large fish monitoring.

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]

Coastal estuaries globally, including the San Francisco Estuary (SFE), are experiencing significant degradation, often resulting in fisheries collapses. The SFE has undergone profound modifications due to population growth, industrialization, urbanization and increasing water exports for human use. These changes have significantly altered the aquatic ecosystem, favouring invasive species and becoming less hospitable to native species such as the longfin smelt (Spirinchus thaleichthys). With longfin smelt abundance declining to <1% of historical numbers, there is a pressing need for laboratory-based experiments aimed at investigating the effects of varying environmental conditions on their stress response and physiology. This study explored the impact of temperature (11 and 14°C) and turbidity maintained with algae (1, 4 and 11 nephelometric turbidity units (NTU)) on the physiological condition of juvenile longfin smelt. Fish were sampled after 2 and 4 weeks in experimental conditions and analysed for whole-body cortisol, glucose, lactate and protein. Condition factor was calculated using length and weight measurements. Critical thermal maximum trials were conducted to assess how prior rearing conditions affected upper thermal tolerance. Cortisol levels were significantly higher in fish held in low-turbidity conditions, whilst glucose levels were significantly greater at lower temperatures and higher turbidities. Protein-to-mass ratios were significantly greater in higher turbidity conditions, with a significant interaction between temperature and turbidity further influencing these ratios. Moreover, 14°C led to diminished condition factors but increased upper thermal tolerances (26.3 ± 0.05 vs 24.6 ± 0.18) compared to longfin smelt at 11°C, highlighting a potential trade-off between the induction of defense mechanisms and subsequent reductions in energy and growth. Data suggest that cooler temperatures (11°C) and elevated turbidities (11 NTU) can benefit juvenile longfin smelt by reducing stress and enhancing growth and energy. These findings hold significant implications for informing and optimizing future endeavours in the culturing and conservation of this species. [ABSTRACT FROM AUTHOR]

Upper thermal limits in many fish species are limited, in part, by the heart's ability to meet increased oxygen demand during high temperatures. Cardiac plasticity induced by developmental temperatures can therefore influence thermal tolerance. Here, we determined how incubation temperatures during the embryonic stage influence cardiac performance across temperatures during the sensitive larval stage of the imperiled longfin smelt. We transposed a cardiac assay for larger fish to newly hatched larvae that were incubated at 9°C, 12°C or 15°C. We measured heart rate over increases in temperature to identify the Arrhenius breakpoint temperature (TAB), a proxy for thermal optimum and two upper thermal limit metrics: temperature when heart rate is maximized (Tpeak) and when cardiac arrhythmia occurs (TArr). Higher incubation temperatures increased TAB, Tpeak and TArr, but high individual variation in all three metrics resulted in great overlap of individuals at TAB, Tpeak and TArr across temperatures. We found that the temperatures at which 10% of individuals reached Tpeak or TArr and temperatures at which number of individuals at TAB relative to Tpeak (ΔN(TAB,Tpeak)) was maximal, correlated more closely with upper thermal limits and thermal optima inferred from previous studies, compared to the mean values of the three cardiac metrics of the present study. Higher incubation temperatures increased the 10% Tpeak and TArr thresholds but maximum ΔN(TAB,Tpeak) largely remained the same, suggesting that incubation temperatures modulate upper thermal limits but not Topt for a group of larvae. Overall, by measuring cardiac performance across temperatures, we defined upper thermal limits (10% thresholds; Tpeak, 14.4–17.5°C; TArr, 16.9–20.2°C) and optima (ΔN(TAB,Tpeak), 12.4–14.4°C) that can guide conservation strategies for longfin smelt and demonstrated the potential of this cardiac assay for informing conservation plans for the early life stages of fish. [ABSTRACT FROM AUTHOR]

The phytoplankton distribution in estuaries is influenced by multiple spatially variable growth and loss processes. As phytoplankton are transported by tidal and net flows, they are exposed to changing conditions of turbidity, depth, temperature, stratification, and grazing. Understanding the factors influencing the observed phytoplankton distribution patterns will allow better-informed restoration and water management efforts. We developed a Lagrangian approach driven by three-dimensional hydrodynamic model results and a simple representation of the production and losses of phytoplankton, allowing a highly efficient closed-form solution for phytoplankton biomass. Our analysis used continuous observations of chlorophyll concentration at four stations and a near-synoptic chlorophyll dataset collected underway from a boat in the channels of Suisun Marsh in the San Francisco Estuary. We divided the study region into four compartments defined by the water depth and location. For each observation location, hydrodynamic model simulations calculated the time that water parcels spent in each of these compartments and the mean depth encountered by water parcels in those compartments. Then, using that information and continuous monitoring data, we inferred compartment-specific grazing rates and two additional ecological parameters. The underway chlorophyll dataset was used for model validation. The model predicted patterns of observed spatial and tidal variability in chlorophyll in Suisun Marsh. The modeling indicated that the chlorophyll concentration at a point in space in time depends largely on the relative exposure to shallow areas, with positive net productivity and deep areas having negative net productivity. [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]

Conversion of wetlands in the Sacramento-San Joaquin Delta beginning in the mid-1800s resulted in a pronounced shift from a wetlanddominated food web to one driven by open-water primary producers. Submersed and floating aquatic vegetation (SAV and FAV) now rank highest in potential net primary production (NPP) among producer groups, and provide a comparable amount of carbon to the detrital food web as marshes. However, important details of this contribution that relate to shifts in species composition and habitat extent were not understood. Here, we review how changes in aquatic vegetation influence NPP and trophic support from the historical to modern periods, within the modern period (the last 2 decades), and under future management and climate scenarios. We estimate that NPP of SAV and FAV during the historical period was approximately half that of today, before increases in open water and introduction of the highly productive water primrose. During the modern period (the last 20 years), high interannual variability in the extent and relative composition of aquatic vegetation species has driven significant variation in total NPP. This recent temporal variation is 6 to 13 times larger than projected changes in production from the potential future scenarios we modeled, including a reduction in FAV by 20% through control measures, substantial wetland restoration (and thus increased channel area that could support SAV and FAV), and increased salinity intrusion in the western Delta with climate warming, which favors native species with greater salinity tolerance. Large temporal swings in NPP of SAV and FAV cascade to influence the degree of carbon that flows to consumers through detrital pathways and herbivory. This volatility and interannual inconsistency in aquatic vegetation support of food webs make achieving wetland restoration goals for the Delta--which could lead to recovery of a portion of the NPP lost since historical times--even more imperative. [ABSTRACT FROM AUTHOR]

Harmful algal blooms (HABs) are on the rise worldwide. Known drivers for the proliferation and intensification of HAB events include increasing nutrient pollution, climate change, regulation and modification of hydrological flow, and the combined effect of climate drivers and nutrient pollution. The San Francisco Bay-Delta system has largely been immune to severe or acute HAB events, but there is both a potential and realized threat which has been underestimated and under-reported, in part because of the lack of coordinated sampling and data reporting. There is also increasing evidence that HABs must be considered in the context of a freshwater-to-marine continuum, and that the physical and political boundaries separating components of the Bay-Delta system are porous barriers to HABs and their toxins. Much remains to be learned about the ecology and physiology of HAB organisms in this system, but five primary environmental drivers can be identified: temperature, salinity, irradiance, nutrients, and stratification/residence time. All these drivers are responding rapidly to climate change, but nutrients are the primary variable that is largely under human control. Plans for the development of a comprehensive monitoring, prediction, and mitigation strategy across the freshwater-to-marine continuum have been documented; effectively following through on these plans provides a roadmap toward identifying the drivers and threats--and reducing the potential consequences now and in the future. While HABs alone are not a sufficient motivator for potentially costly and extensive mitigation efforts, there is strong evidence that decreasing nutrient loads, maintaining hydrological connectivity while minimizing stagnant regions, and managing the biota to maintain biodiversity of the Bay-Delta system will result in multiple co-benefits, including reduction of the HAB threat potential. [ABSTRACT FROM AUTHOR]

The Longfin Smelt (LFS, Spirinchus thaleichthys) population within the San Francisco Estuary, California, has experienced a substantial reduction, diminishing to <1% of their historical abundance. This decline has culminated in their classification as a threatened species under the purview of the California Endangered Species Act. Understanding their physiology and stress response in relation to varying environmental conditions, such as temperature and turbidity, is crucial for LFS culturing, management, and conservation. In this study, we assessed juvenile LFS (age range during exposure: 181 to 228 days post hatch, dph) performance as measured by growth and gene expression following four weeks at two temperatures (11 °C and 14 °C) and three turbidity levels (1, 4, and 11 nephelometric turbidity units (NTU)). At the end of the 4-week exposure period, we conducted assessments encompassing fork length, wet weight, condition factor, and examined alterations in the transcription of 12 genes. The selection of these genes aimed at determining responses associated with osmoregulation, growth, metabolism, and general stress, as all of which are potentially influenced by temperature and/or turbidity. Weight and condition factor was significantly higher at lower temperature, whereas turbidity had no effect on growth, condition factor, and transcriptomic stress-response. Instead, the lower expression levels of Catalase , Citrate Synthase and Growth Factor Receptor Bound Protein 10 at 14 °C were indicative of metabolic and growth-related changes governed by temperature. This suggests that rearing of LFS at 11 °C and low turbidity (<11 NTU) is suitable for the juvenile stage, whereas growth as well as metabolic capacity is limited at slightly warmer temperatures. • Juvenile Longfin Smelt exhibited increased growth at 11 °C compared to 14 °C. • Turbidity levels of up to 11 NTU demonstrated no discernible impact juvenile Longfin Smelt. • Rearing of juvenile Longfin Smelt at 11 °C and at low turbidity (<11NTU) is adequate for captive culture. [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]

The San Francisco Estuary (SFE) is one of the most degraded ecosystems in the United States, and organisms that inhabit it are exposed to a suite of environmental stressors. The delta smelt (Hypomesus transpacificus), a small semi-anadromous fish endemic to the SFE and considered an indicator species, is close to extinction in the wild. The goal of this study was to investigate how environmental alterations to the SFE, such as reductions in turbidities, higher temperatures and increased prevalence of invasive predators affect the physiology and stress response of juvenile delta smelt. Juvenile delta smelt were exposed to two temperatures (17 and 21°C) and two turbidities (1–2 and 10–11 NTU) for 2 weeks. After the first week of exposure, delta smelt were exposed to a largemouth bass (Micropterus salmoides) predator cue at the same time every day for 7 days. Fish were measured and sampled on the first (acute) and final (chronic) day of exposures to predator cues and later analyzed for whole-body cortisol, glucose, lactate, and protein. Length and mass measurements were used to calculate condition factor of fish in each treatment. Turbidity had the greatest effect on juvenile delta smelt and resulted in reduced cortisol, increased glucose and lactate, and greater condition factor. Elevated temperatures reduced available energy in delta smelt, indicated by lower glucose and total protein, whereas predator cue exposure had negligible effects on their stress response. This is the first study to show reduced cortisol in juvenile delta smelt held in turbid conditions and adds to the growing data that suggest this species performs best in moderate temperatures and turbidities. Multistressor experiments are necessary to understand the capacity of delta smelt to respond to the multivariate and dynamic changes in their natural environment, and results from this study should be considered for management-based conservation efforts. [ABSTRACT FROM AUTHOR]

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non‐native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping. [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]

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 (https://marinescience.ucdavis.edu/engagement/past-events/edna). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods. [ABSTRACT FROM AUTHOR]

Estuaries are ecologically and economically important ecosystems but are threatened by non-native invasive species, including many species of submersed aquatic vegetation (SAV). Herbicides are the primary tool used to control SAV, but most field evaluations of herbicides have been conducted in lentic systems. Therefore, managers working in estuaries must base their SAV control programs largely on findings from systems fundamentally different from their own. We conducted a study in the Sacramento-San Joaquin Delta to determine efficacy of the widely used herbicide fluridone in an estuarine ecosystem. The primary goal of SAV removal was restoration of open water habitat for endangered Hypomesus transpacificus (Delta Smelt). Over 18 months and multiple sets of multi-week fluridone applications, we monitored concentrations of fluridone and responses by SAV across pairs of treated and reference sites. Fluridone concentrations in the water were generally below the 2–5 parts per billion required for SAV control. Monitoring demonstrated that these low water concentrations were likely due to dissipation by tides, despite use of pelleted fluridone formulations marketed for flowing water environments. Fluridone did, however, accumulate in sediment at concentrations hundreds of times higher than those measured in the water. Nonetheless, we did not observe lasting reductions in SAV abundance or changes in SAV community composition. By demonstrating lack of efficacy of one of the few herbicides permitted for use in this estuary, this study highlights the need for development of SAV management tools tailored to the challenges of hydrologically complex environments like estuaries. [ABSTRACT FROM AUTHOR]

Abstract Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non‐native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping.

Quantitative, broadly applicable metrics of resilience are needed to effectively manage tidal marshes into the future. Here we quantified three metrics of temporal marsh resilience: time to marsh drowning, time to marsh tipping point, and the probability of a regime shift, defined as the conditional probability of a transition to an alternative super-optimal, suboptimal, or drowned state. We used organic matter content (loss on ignition, LOI) and peat age combined with the Coastal Wetland Equilibrium Model (CWEM) to track wetland development and resilience under different sea-level rise scenarios in the Sacramento-San Joaquin Delta (Delta) of California. A 100-year hindcast of the model showed excellent agreement (R2 = 0.96) between observed (2.86 mm/year) and predicted vertical accretion rates (2.98 mm/year) and correctly predicted a recovery in LOI (R2 = 0.76) after the California Gold Rush. Vertical accretion in the tidal freshwater marshes of the Delta is dominated by organic production. The large elevation range of the vegetation combined with high relative marsh elevation provides Delta marshes with resilience and elevation capital sufficiently great to tolerate centenary sea-level rise (CLSR) as high as 200 cm. The initial relative elevation of a marsh was a strong determinant of marsh survival time and tipping point. For a Delta marsh of average elevation, the tipping point at which vertical accretion no longer keeps up with the rate of sea-level rise is 50 years or more. Simulated, triennial additions of 6 mm of sediment via episodic atmospheric rivers increased the proportion of marshes surviving from 51% to 72% and decreased the proportion drowning from 49% to 28%. Our temporal metrics provide critical time frames for adaptively managing marshes, restoring marshes with the best chance of survival, and seizing opportunities for establishing migration corridors, which are all essential for safeguarding future habitats for sensitive species.

Spatial subsidies and habitat connectivity are critical factors in estuarine trophic webs. Advection and tidal dispersion of organic matter including plankton from productive regions such as wetlands can subsidize consumers in less productive areas. These dispersive fluxes have generally been assumed to result from tidal mixing along concentration gradients, but other mechanisms of dispersion may be important. We estimated fluxes of the calanoid copepod Pseudodiaptomus forbesi between a restored marsh and a connected channel in the northern San Francisco Estuary in summer 2018 using continuous flow data and hourly abundance data over four tidal cycles. Late copepodites and adults were demersal, abundant in the water column only at night, and abundance was uncorrelated with tidal flows. Over the tidal day, dispersive fluxes of copepods were variable. However, over the entire summer, tidal flows were flood dominant at night when the copepods were in the water column, driving an estimated dispersive flux into the marsh. Dispersion at the marsh will change seasonally as tidal patterns and copepod abundance change. Our results show that the transport of zooplankton in shallow tidal systems is regulated by the interactions of diel zooplankton behavior with long-term tidal patterns. Similar interactions in other systems will result in transport based on site-specific hydrodynamics and zooplankton behavior, and could move zooplankton up the concentration gradient rather than down. Patterns of zooplankton behavior and currents occur on a wide variety of time scales; thus, researchers must take a long-term perspective to understand these interactions. [ABSTRACT FROM AUTHOR]

Following its listing as threatened under the California Endangered Species Act in 2009, Longfin Smelt (Spirinchus thaleichthys) became a focus of resource managers in the San Francisco Estuary. Water exports were identified as one of the factors affecting Longfin Smelt abundance, and managers were challenged with balancing freshwater flows through the Sacramento-San Joaquin River Delta between human and ecosystem needs. This balance becomes especially challenging during the winter and spring when Longfin Smelt are spawning. Resource managers identified that the impact associated with entrainment of larval Longfin Smelt in the winter was uncertain, and to understand and manage this risk, new data was needed. In 2009 the Smelt Larva Survey was implemented and has since sampled newly hatched larvae from January–March. Here, I analyze this data and ask specific questions regarding distribution and densities of the larvae throughout five regions of the Upper Estuary – Napa River, Suisun, Confluence, Northern Delta, and Southern Delta – with the goal of understanding the spatial and temporal patterns of larval distribution since 2009. I found that larvae were most prevalent in the Suisun, Confluence, and Northern Delta regions, and less common in the Southern Delta and Napa River regions. Larval Longfin Smelt densities changed following a recent drought and record low population abundances. Median per-station averaged densities ranged from 154 to 274 fish per 1,000 m3 between 2009 and 2013 but declined to 1 to 65 fish per 1,000 m3 from 2014 to 2019. This survey data demonstrates that Longfin Smelt reproductive output has declined since their listing in 2009 and that their distribution into the Southern Delta is low relative to the rest of the Upper Estuary. These results reaffirm the species’ continued decline since its listing, and that improving the abundance of spawning adults is one of the many important steps needed for long-term recovery and resilience.

Climate change may cause organisms to seek thermal refuge from rising temperatures, either by shifting their ranges or seeking microrefugia within their existing ranges. We evaluate the potential for thermal stratification to provide refuge for two fish species in the San Francisco Estuary (Estuary): Chinook Salmon (Oncorhynchus tshawytscha Walbaum, 1792) and Delta Smelt (Hypomesus transpacificus McAllister, 1963). We compiled water temperature data from multiple monitoring programs to evaluate spatial, daily, hourly, intra-annual, and inter-annual trends in stratification using generalized additive models. We used our models to predict the locations and periods of time that the bottom of the water column could function as thermal refuge for salmon and smelt. Periods in which the bottom was cooler than surface primarily occurred during the peak of summer and during the afternoons, with more prominent stratification during warmer years. Although the Estuary is often exceedingly warm for fish species and well-mixed overall, we identified potential thermal refugia in a long and deep terminal channel for Delta Smelt, and in the periods bordering summer for Chinook Salmon. Thermal stratification may increase as the climate warms, and pockets of cooler water at depth, though limited, may become more important for at-risk fishes in the future. [ABSTRACT FROM AUTHOR]

Wetland restoration is a key management tool for increasing food availability for at-risk fishes in the San Francisco Estuary. To characterize the benefits of restoration sites, it is critical to quantify the abundance and composition of fish food resources in and near the wetlands. Characterization of zooplankton communities is considered particularly important, but accurate analysis of zooplankton samples is time-consuming and expensive. The recently established Fish Restoration Program (FRP) Monitoring Team assessed whether data from existing long-term monitoring surveys could be used to characterize shallow-water zooplankton communities before restoration. During the springs of 2017 to 2019, the FRP collected zooplankton samples near the mouth of tidal wetland sites, or immediately outside future restoration sites, and compared them to concurrent samples collected in deep water by existing long-term monitoring surveys. We found very few differences in community composition between shallow and deep samples, though a few taxa were more abundant in shallow water. Seasonal and interannual differences in composition and abundance showed that restoration sites provide varying food resources over time. There was significantly higher total abundance of zooplankton in deep versus shallow water, which may be a result of differences in zooplankton production, migration, or fish predation. Inconsistencies in towing speed and gear type may also be driving this result, rather than true habitat differences. This study indicates that monitoring of wetland restoration sites must rely on multiple years of data collected on the site--rather than relying on adjacent open-water sampling--and should include monitoring of epiphytic and epibenthic invertebrates as well as zooplankton. [ABSTRACT FROM AUTHOR]

The density and quality of zooplankton prey affect the feeding success of larval and juvenile fishes and thus can drive growth, survival, and recruitment. As part of a larger effort investigating potential causes of a pelagic fish decline, we examined regional feeding success (food presence/absence, stomach fullness), diet composition and prey selection of young Longfin Smelt (Spirinchus thaleichthys) in spring and summer as a function of fish size and prey availability in the San Francisco Estuary. We conducted our sampling during two wet and two dry years, because weather and river flow influence prey community composition and location. Larval and juvenile fish showed evidence of food limitation: high proportions of empty stomachs (≤ 70%) and stomach contents totaling

Gill-net size selectivity for 15 fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies, which together contained 7,096 individual fish observations from 882 gill-net sets. The gill nets considered in this study closely resembled the American Fisheries Society's recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in gill nets were estimated indirectly using generalized linear modeling and maximum likelihood. Selectivity curves are provided for each species to inform researchers about the population characteristics of fishes sampled with similar gill nets. [ABSTRACT FROM AUTHOR]

Understanding life-history diversity in a population is imperative to developing effective fisheries management and conservation practices, particularly in degraded environments with high environmental variability. Here, we examined variation in habitat use and migration patterns of White Sturgeon (Acipenser transmontanus), a long-lived migratory fish that is native to the San Francisco Estuary, CA, United States. Annual increment profiles were combined with respective geochemical (87Sr/86Sr) profiles in sturgeon fin rays to reconstruct annual salinity chronologies for 112 individuals from 5 to 30 years old. Results indicated a complex and diverse amphidromous life history across individuals, characterized largely by estuarine residence, a general ontogenetic trend toward higher-salinity brackish habitats, and high variability in habitat use across all age groups. Hierarchical clustering based on fin ray geochemistry during the first 10 years of life, prior to sexual maturation, indicated at least four distinct migratory phenotypes which differed largely in the timing and duration of juvenile to subadult movements between fresh- and brackish-water habitats. This study provides information regarding habitat use and migration in sub-adult fish that was previously lacking. Different migratory phenotypes vary in exposure to stressors across time and space and populations. Understanding White Sturgeon habitat distributions through space and time at different life stages can help identify areas where habitat restoration would be most effective and develop management actions to reduce stressors associated with specific areas where White Sturgeon are present.

Longfin smelt (Spirinchus thaleichthys) is a threatened anadromous fish species that spawns in freshwater to moderately brackish (i.e. 5–10 ppt) reaches of the upper San Francisco Estuary and has declined to ~1% of its pre-1980s abundances. Despite 50+ years of population monitoring, the efficacy of 10+ years of conservation efforts for longfin smelt remain uncertain due to a limited understanding of how the species responds to environmental variation, such as salinity. For example, high mortality during larval stages has prevented culture efforts from closing the life cycle in captivity. Here, we investigated the effects of salinity on longfin smelt yolk-sac larvae. Newly hatched larvae from four single-pair crosses were acutely transferred to and reared at salinities of 0.4, 5, 10, 20 or 32 ppt. We compared whole-body water and sodium ion (Na+) content, notochord length and yolk-sac volume at 12, 24, 48, 72, and 96 hours post-transfer for each salinity treatment. We found that larvae maintained osmotic and ionic balance at 0.4–10 ppt, whereas salinities ˃10 ppt resulted in decreased water and increased whole-body Na+ content. We also found that larvae grew largest and survived the longest when reared at 5 and 10 ppt, respectively, and that yolk resorption stalled at 0.4 ppt. Finally, there were significant but small interclutch variations in responses to different salinities, with clutch accounting for <8% of the variance in our statistical models. Overall, our results indicate that longfin smelt yolk-sac larvae likely perform best at moderately brackish conditions, thus yielding a mechanism that explains their distribution in field surveys and providing key information for future conservation efforts. [ABSTRACT FROM AUTHOR]

Pathogen surveillance must be part of any population supplementation or reintroduction program for the conservation of threatened and endangered species. The unintended transmission of pathogens can have devastating effects on these already at-risk populations or the natural ecosystem at large. In the San Francisco Estuary (estuary), abundance of the endemic Delta Smelt (Hypomesus transpacificus) has declined to the point where regulatory managers are preparing to augment the wild population using fish propagated in a hatchery to prevent species extinction. Although disease is not an overt cause of population decline, comprehensive pathogen presence and prevalence data are lacking. Here, we performed a pilot study that applied molecular assays originally developed in salmonids to assess the presence of a wide variety of pathogens in the gill tissue of cultured and wild Delta Smelt--as well as cultured fish--deployed in enclosures in the estuary. We found the assays to be highly sensitive, and observed positive detections of a single pathogen, Ichthyophthirius multifiliis, in 13% of cultured Delta Smelt. We also detected ten other pathogens at very low levels in cultured, enclosure-deployed, and wild Delta Smelt that likely represent the ambient pathogen composition in the estuary (as opposed to actual infection). Our results corroborate previous work that cultured Delta Smelt do not appear to present a high risk for pathogen transmission during population supplementation or reintroduction. However, the molecular pathogen screening assays tested here have great utility as an early warning system indicator of when further diagnostic testing might be necessary to limit the extent and frequency of disease outbreaks; their utility will be further increased once they are customized for Delta Smelt. [ABSTRACT FROM AUTHOR]

Suspended-sediment flux at the ocean boundary of the San Francisco Estuary—the Golden Gate—was measured over a tidal cycle following peak watershed runoff from storms to the estuary in two successive years to investigate sediment transport through the estuary. Observations were repeated during low-runoff conditions, for a total of three field campaigns. Boat-based measurements of velocity and acoustic backscatter were used to calculate water and suspended-sediment flux at a location 1 km landward of the Golden Gate. Suspended-sediment concentration (SSC) and salinity data from up-estuary sensors were used to track watershed-sourced sediment plumes through the estuary. Estimates of suspended-sediment load from the watershed and net suspended-sediment flux for one up-estuary subembayment were used to infer in-estuary trapping of sediment. For both post-storm field campaigns, observations at the ocean boundary were conducted on the receding limb of the watershed hydrograph. At the ocean boundary, peak instantaneous suspended-sediment flux was tidally asymmetric and was greater on flood tides than on ebb tides for all three field campaigns, due to higher average SSC in the cross-section on flood tides. Shear-induced sediment resuspension was greater on flood tides and suggests the presence of an erodible pool outside the estuary. The storms in 2016 led to less export of discharge and sediment from the watershed and greater sediment trapping within one up-estuary subembayment compared to that observed in 2017. Results suggest that substantial trapping of watershed sediments occurred during both storm events, likely due to the formation of estuarine turbidity maxima (ETM) at different locations in the estuary. ETM locations were forced nearer the ocean boundary in 2017. Additional measurements and modeling are required to quantify the long-term sediment flux at the Golden Gate. [ABSTRACT FROM AUTHOR]

Estuaries worldwide are experiencing stress due to increased droughts, which often prompt intervention by environmental managers and government agencies. Effective management of water resources in estuarine systems can be enhanced by new technologies and methodologies to support decision-making processes. Here, we evaluate the use of high-frequency, high-resolution satellite remote sensing within two managementrelevant case studies in the San Francisco Estuary and the Sacramento--San Joaquin River Delta. We used a remote sensing-derived time series of turbidity maps to (1) identify favorable turbidity conditions for the endangered fish species, delta smelt (Hypomesus transpacificus), during the height of the great California drought in the dry season of 2015, and (2) evaluate changes in turbidity following the installation of an emergency saltwater intrusion barrier. The mapping results indicate several persistent areas of turbidity refugia throughout the summer in the north and west Delta; however, there was infrequent connectivity. A comparison of images captured during ebb tides before and after barrier installation showed a mean increase of 6.6 Nephelometric Turbidity Units (NTU) in the San Joaquin River and 4 NTU in Fisherman's Cut. Our assessment of the barrier supports previous findings, which used field samples to conclude barrier installation may have resulted in increased turbidity near the barrier and enhances these findings by providing spatial context. [ABSTRACT FROM AUTHOR]

This study utilizes satellite data to investigate water quality conditions in the San Francisco Estuary and its upstream delta, the Sacramento--San Joaquin River Delta. To do this, this study derives turbidity from the European Space Agency satellite Sentinel-2 acquired from September 2015 to June 2019 and conducts a rigorous validation with in situ measurements of turbidity from optical sensors at continuous monitoring stations. This validation includes 965 matchup comparisons between satellite and in situ sensor data across 22 stations, yielding R² = 0.63 and 0.75 for Nephelometric Turbidity Unit and Formazin Nephelometric Unit (FNU) stations, respectively. This study then applies remote sensing to evaluate patterns in turbidity during the Suisun Marsh Salinity Control Gates Action ("Gates action"), a pilot study designed to increase habitat access and quality for the endangered Delta Smelt. The basic strategy was to direct more freshwater into Suisun Marsh, creating more low salinity habitat that would then have higher (and more suitable) turbidity than upstream river channels. For all seven acquisitions considered from June 29 to September 27, 2018, turbidity conditions in Bays and Sloughs subregions were consistently higher (and more suitable) (26-47 FNU) than what was observed in the upstream River region (13-25 FNU). This overall pattern was observed when comparing images acquired during similar tidal stages and heights. [ABSTRACT FROM AUTHOR]

This work surveys the performance of several empirical models, all recalibrated to a common data set, that were developed over the past 25 years to relate freshwater flow and salinity in the San Francisco Estuary (estuary). The estuary's salinity regime--broadly regulated to meet urban, agricultural, and ecosystem beneficial uses--is managed in spring and certain fall months to meet ecosystem objectives by controlling the 2 parts per thousand bottom salinity isohaline position (referred to as X2). We tested five empirical models for accuracy, mean, and transient behavior. We included a sixth model, employing a machine learning framework and variables other than outflow, in this survey to compare fitting skill, but did not subject it to the full suite of tests applied to the other five empirical models. Model performance was observed to vary with hydrology, year, and season, and in some cases exhibited unique limitations as a result of mathematical formulation. However, no single model formulation was found to be consistently superior across a wide range of tests and applications. One test revealed that the models performed equally well when recalibrated to a uniformly perturbed input time-series. Thus, while the models may be used to identify anomalies or seasonal biases (the latter being the subject of a companion paper), their use as inverse models to infer freshwater outflow to the estuary from salinity observations is not expected to improve upon the absolute accuracy of existing outflow estimates. This survey suggests that, for analyses that span a long hydrologic record, an ensemble approach--rather than the use of any individual model on its own--may be preferable to exploit the strengths of individual models. [ABSTRACT FROM AUTHOR]

Recent modeling has demonstrated that sediment supply is one of the primary environmental variables that will determine the sustainability of San Francisco Estuary tidal marshes over the next century as sea level rises. Therefore, understanding the environmental controls on sediment flux within the San Francisco Estuary is crucial for optimal planning and management of tidal marsh restoration. Herein, we present suspended-sediment flux estimates from water year (WY) 2009–2016 from the San Francisco Estuary to investigate the environmental controls and impact of the record 2013–2016 California drought. During the recent drought, sediment flux into Lower South Bay, the southernmost subembayment of the San Francisco Estuary, increased by 345% from 114 kt/year from WY 2009 to 2011 to 508 kt/year from WY 2014 to 2016, while local tributary sediment flux declined from 209 to 51 kt/year. Total annual sediment flux from WY 2009 to 2011 and 2014 to 2016 can be predicted by total annual freshwater inflow from the Sacramento-San Joaquin Delta (R2 = 0.83, p < 0.01), the primary source of freshwater input into the San Francisco Estuary. The volume of freshwater inflow from the Sacramento-San Joaquin Delta is hypothesized to affect shoal-to-channel density gradients that affect sediment flux from broad, typically more saline and turbid shoals, to the main tidal-channel seaward of Lower South Bay. During the drought, freshwater inflow from the Sacramento-San Joaquin Delta decreased, and replacement of typically more saline shoal water was reduced. As a result, landward-increasing cross-channel density gradients enhanced shoal-to-channel advective flux that increased sediment available for tidal dispersion and drove an increase in net-landward sediment flux into Lower South Bay. [ABSTRACT FROM AUTHOR]

Hydrodynamic processes can lead to the accumulation and/or dispersal of water column constituents, including sediment, phytoplankton, and particulate detritus. Using a combination of field observations and stable isotope tracing tools, we identified how hydrodynamic processes influenced physical habitat, pelagic communities, and food web structure in a freshwater tidal system. The pelagic habitat of a terminal channel differed spatially, likely aligning with differences in hydrodynamics. Three zones that we classified by exchange with downstream habitat had distinct water quality characteristics, supported different densities of zooplankton and nekton, and exhibited disparate support from benthic and pelagic trophic pathways to pelagic consumers. Hydrodynamically driven zones and their emergent characteristics appeared sensitive to hydrology, as elevated runoff was correlated with a shift in hydrodynamic habitat and organismal distributions. The results of our study highlight the relationship between hydrodynamic processes, biological responses, and climate, and suggest that understanding the physical process can improve understanding of pelagic habitats and communities. [ABSTRACT FROM AUTHOR]

State‐space models (SSMs) are a popular tool for modeling animal abundances. Inference difficulties for simple linear SSMs are well known, particularly in relation to simultaneous estimation of process and observation variances. Several remedies to overcome estimation problems have been studied for relatively simple SSMs, but whether these challenges and proposed remedies apply for nonlinear stage‐structured SSMs, an important class of ecological models, is less well understood. Here we identify improvements for inference about nonlinear stage‐structured SSMs fit with biased sequential life stage data. Theoretical analyses indicate parameter identifiability requires covariates in the state processes. Simulation studies show that plugging in externally estimated observation variances, as opposed to jointly estimating them with other parameters, reduces bias and standard error of estimates. In contrast to previous results for simple linear SSMs, strong confounding between jointly estimated process and observation variance parameters was not found in the models explored here. However, when observation variance was also estimated in the motivating case study, the resulting process variance estimates were implausibly low (near‐zero). As SSMs are used in increasingly complex ways, understanding when inference can be expected to be successful, and what aids it, becomes more important. Our study illustrates (a) the need for relevant process covariates and (b) the benefits of using externally estimated observation variances for inference about nonlinear stage‐structured SSMs. [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]

The San Francisco Estuary is an incredibly diverse ecosystem with a mosaic of aquatic habitats inhabited by a number of economically, culturally, and ecologically important fish species. To monitor the temporal and spatial trends of this rich fish community, long-term fish monitoring programs within the estuary use a variety of gear types to capture fish species across life stages and habitats. However, concerns have been raised that current sampling gears may fail to detect certain species--or life stages--that inhabit areas that are not accessible by current gear types (e.g., riprap banks, shallow vegetated areas). Boat electrofishing is one sampling method that has been proposed to supplement current long-term fish monitoring in the upper estuary. In this study, we used fish catch data from past boat electrofishing studies, a long-term beach seine survey, and a couple of long-running trawl surveys to compare the relative probability of detecting various fishes across these sampling gears. Overall, we found that boat electrofishing led to notable improvements in the detection rates for many native and non-native fishes we examined. Boat electrofishing gear was better at detecting the majority of species in the spring (20 out of 38 species, 53%) and fall-winter (24 out of 34 species, 70%) sampling periods. Based on these findings, we recommend that resource managers consider the implementation of a long-term boat electrofishing survey to help them in their long-term conservation planning for fishes within the upper estuary. [ABSTRACT FROM AUTHOR]

Managing endangered species is challenging when increased rarity leads to an inability to detect their responses to environmental conditions. In the San Francisco Estuary, the state and federally listed Delta Smelt (Hypomesus transpacificus) has declined to record low numbers, elevating concern over entrainment at the State Water Project (SWP) and Central Valley Project (CVP) water export facilities. The objective of this study was to: (1) revisit previous work on factors that affect adult Delta Smelt collected at the SWP and CVP fish collection facilities using updated conceptual models and a new statistical approach; and (2) to determine factors that affect salvage at time-scales of interest to management. Boosted Regression Tree (BRT) models were applied to salvage data at the SWP and CVP, aggregated into two response categories: a "first flush" response that represented daily salvage from the start of the entrainment window to the 50% midpoint of observed salvage, and a "seasonal" response that included daily salvage from the entire entrainment window. Precipitation, sub-adult abundance, Yolo Bypass flow, and exports best explained first flush salvage at both the SWP and CVP. The seasonal models included a similar set of influential variables, but the relative influence of precipitation was lower compared to the first flush models., Yolo Bypass flow was more influential for seasonal salvage at the SWP, compared to the CVP; Old and Middle River flow was more influential for seasonal salvage at the CVP. Although the rank of variable importance that explains salvage differed slightly between first flush and seasonal time-scales, this study suggests that salvage is most influenced by hydrodynamics, water quality, and population abundance. The application of BRT models to predict salvage is limited, because salvage has been low since federal protections were implemented in 2008. Forecast models that integrate real-time variables with fish behavior models may improve Delta Smelt management. [ABSTRACT FROM AUTHOR]

In this study, we investigate how changes in the vertical distribution of suspended sediment affect continuous suspended sediment flux measurements at a location in the San Francisco Estuary. Current methods for measuring continuous suspended sediment flux estimates relate continuous estimates of suspended-sediment concentration (SSC) measured at-a-point (SSCpt) to discrete cross-section measurements of depth-averaged, velocity-weighted SSC (SSCxs). Regressions that compute SSCxs from continuous estimates of SSCpt require that the slope between SSCpt and SSCxs, controlled by the vertical distribution of SSC, is fixed. However, in tidal systems with suspended cohesive sediment, factors that control the vertical SSC profile—vertical turbulent mixing and downward settling of suspended sediment mediated by flocculation of cohesive sediment—constantly vary through each tide and may exhibit systematic differences between flood and ebb tides (tidal asymmetries in water velocity or particle size). We account for changes in the vertical SSC profile on estimates of SSCxs using time series of the Rouse number of the Rouse-Vanoni-Ippen equation combined with optical turbidity measurements, a surrogate for SSCpt, to predict SSCxs from 2009 to 2011 and 2013. Time series of the Rouse number were estimated by fitting the Rouse-Vanoni-Ippen equation to SSC estimated from optical-turbidity measurements taken at two elevations in the water column. When accounting for changes in the vertical SSC profile, changes in not only the magnitude but also the direction of cumulative sediment-flux measurements were observed. For example, at a mid-depth sensor, sediment flux estimates changed from − 319 kt (± 65 kt, negative indicating net seaward transport) to 482 kt (± 140 kt, positive indicating net landward transport) for 2009–2011 and from − 388 kt (± 140 kt) to 1869 kt (± 406 kt) for 2013–2016. At the study location, estimation of SSCxs solely from SSCpt resulted in sediment flux values that were underestimates on flood tides and overestimates on ebb tides. This asymmetry is driven by covariance between water velocity and particle settling velocity (Ws) with larger Ws on flood compared to ebb tides. Results of this study indicate that suspended-sediment-flux measurements estimated from point estimates of SSC may be biased if systematic changes in the vertical distribution of SSC are unaccounted for. [ABSTRACT FROM AUTHOR]

Combined water exports from Old River in the south end of California's San Francisco Estuary (estuary) by state and federal pumping facilities entrain small fishes, including out-migrating juvenile salmon. Both export projects have fish salvage facilities that use behavioral barriers (louvers) in combination with screens to guide fish into collection areas from which they are trucked to release points in the western Delta. Sacramento River-origin Chinook Salmon are regularly taken in the projects' fish salvage operations. Survival has been estimated within the boundaries of both intake structures, but not in Old River. Prevailing methods for estimating fish losses are based on studies of louver efficiency, near-field survival at the state facility, and assumed survival at the federal facility. The efficiency of the fish salvage operations is affected by several factors, including intake velocity, debris build-up on the louvers and trash racks, and by the omnipresence of predators in front of and within the fish guidance structures. Analysis of existing data suggests that under average conditions, juvenile salmon survive entrainment into the forebay of the state facility at a rate of less than 10%. There is no evidence for better survival at the federal facility. We found no data on predation outside of either the state's forebay or the federal trash boom, structures which are separated by an approximately 2-km reach of Old River where predation on small fish is thought to be intense. We suggest an improvement to the existing loss estimation, and discuss some features of the studies needed to increase its accuracy and precision. [ABSTRACT FROM AUTHOR]

Recruitment of estuarine organisms can vary dramatically from year to year with abiotic and biotic conditions. The San Francisco Estuary (California, USA) supports a dynamic ecosystem that receives freshwater flow from numerous tributaries that drain one of the largest watersheds in western North America. In this study, we examined distribution and habitat use of two forage fish larvae of management interest, Longfin Smelt Spirinchus thaleichthys and Pacific Herring Clupea pallasii, during a low-flow and a high-flow year to better understand how their rearing locations (region and habitat) may affect their annual recruitment variability. During the low-flow year, larval and post-larval Longfin Smelt were distributed landward, where suitable salinity overlapped with spawning habitats. During the high-flow year, larval Longfin Smelt were distributed seaward, with many collected in smaller tributaries and shallow habitats of San Francisco Bay. Local spawning and advection from seaward habitats were speculated to be the primary mechanisms that underlie larval Longfin Smelt distribution during the high-flow year. Larval Pacific Herring were more abundant seaward in both years, but a modest number of larvae were also found landward during the lowflow year. Larval Pacific Herring abundance was lower overall in the high-flow year, suggesting advection out of the area or poor recruitment. Future monitoring and conservation efforts for Longfin Smelt and Pacific Herring should recognize that potential mechanisms underlying their recruitment can vary broadly across the San Francisco Estuary in any given year, which suggests that monitoring and research of these two species expand accordingly with hydrologic conditions that are likely to affect their spawning and larval rearing distributions. [ABSTRACT FROM AUTHOR]

Understanding how environmental factors—here, light intensity and turbidity—influence the feeding, growth, and survival of larval Delta Smelt is critical for optimizing the culture of this endangered fish species. Three sets of rearing trials were conducted where larvae were cultured under different levels of turbidity and light intensity. Delta Smelt larvae feeding activity was observed throughout the initial adjustment of light and turbidity levels to ascertain feeding ability and behavior at the different levels. It was found that there is a minimum threshold of combined light and turbidity to generate their exogenous feeding response. At low turbidity conditions, early-stage larvae begun feeding and growing earlier when light levels were higher. The condition factor and survival of the late-stage larvae was increased with increased turbidity. The results suggest Delta Smelt larvae may be cultured under lower turbidity and light conditions rather than at the currently used levels. We conclude that the interaction between turbidity and light intensity plays an important role in the feeding activity, growth, and survival of larvae. The results here may inform fish culture lab methodologies, but may also provide useful baseline knowledge for light and turbidity preferences of Delta Smelt larvae in the wild. [ABSTRACT FROM AUTHOR]

Many fishes in the San Francisco Estuary have suffered declines in recent decades, as shown by numerous long-term monitoring programs. A long-term monitoring program, such as the Interagency Ecological Program, comprises a suite of surveys, each conducted by a state or federal agency or academic institution. These types of programs have produced rich data sets that are useful for tracking species trends over time. Problems arise from drawing conclusions based on one or few surveys because each survey samples a different subset of species or reflects different spatial or temporal trends in abundance. The challenges in using data sets from these surveys for comparative purposes stem from methodological differences, magnitude of data, incompatible data formats, and end-user preference for familiar surveys. To improve the utility of these data sets and encourage multisurvey analyses, we quantitatively rate these surveys based on their ability to represent species trends, present a methodology for integrating long-term data sets, and provide examples that highlight the importance of expanded analyses. We identify areas and species that are undersampled, and compare fish salvage data from large water export facilities with survey data. Our analysis indicates that while surveys are redundant for some species, no two surveys are completely duplicative. Differing trends become evident when considering individual and aggregate survey data, because they imply spatial, seasonal, or gear-dependent catch. Our quantitative ratings and integrated data set allow for improved and better-informed comparisons of species trends across surveys, while highlighting the importance of the current array of sampling methodologies. [ABSTRACT FROM AUTHOR]

Suisun Marsh (Solano County, California) is the largest contiguous marsh remaining on the West Coast of the United States, and makes up approximately 10% of the wetlands remaining in the San Francisco Estuary. Suisun Marsh has been safeguarded from development through the operation of over 100 privately owned waterfowl hunting clubs, which manage for diked waterfowl habitat. However, this management—and the subsequent loss of tidal influence—has been considered harmful for some species, including the endangered salt marsh harvest mouse (SMHM; Reithrodontomys raviventris). To determine the value of tidal wetlands relative to those managed for waterfowl, we performed periodic surveys for rodents in managed and tidal wetlands over 5 years, and used capture-mark-recapture analyses to estimate demographic parameters and abundance for the three most common rodents—the northern SMHM (R. r. halicoetes), the western harvest mouse (a sympatric native species; R. megalotis, WHM), and the house mouse (a sympatric invasive species; Mus musculus). Wetland type had no effect on detection, temporary emigration, or survival for any of these species. However, fecundity and population growth for all three species were affected by an interaction of season and wetland type, although none of these parameters was consistently superior in either habitat type. Estimated abundance of SMHM and Mus was similar in both wetland types, whereas WHM were more abundant in managed wetlands. Salt marsh harvest mice also showed no affinity for any microhabitat characteristics associated with tidal wetlands. Managed wetlands in Suisun Marsh support SMHM and Mus equally, and abundances of WHM were greater than in tidal wetlands, suggesting managed wetlands may be superior in terms of supporting native rodents. As climate change and sea level rise are predicted to threaten coastal marshes, these results suggest the recovery strategy for SMHM could incorporate managed wetlands. [ABSTRACT FROM AUTHOR]

Suisun Marsh (Solano County, California) is the largest contiguous marsh remaining on the West Coast of the United States, and makes up approximately 10% of the wetlands remaining in the San Francisco Estuary. Suisun Marsh has been safeguarded from development through the operation of over 100 privately owned waterfowl hunting clubs, which manage for diked waterfowl habitat. However, this management—and the subsequent loss of tidal influence—has been considered harmful for some species, including the endangered salt marsh harvest mouse (SMHM; Reithrodontomys raviventris). To determine the value of tidal wetlands relative to those managed for waterfowl, we performed periodic surveys for rodents in managed and tidal wetlands over 5 years, and used capture-mark-recapture analyses to estimate demographic parameters and abundance for the three most common rodents—the northern SMHM (R. r. halicoetes), the western harvest mouse (a sympatric native species; R. megalotis , WHM), and the house mouse (a sympatric invasive species; Mus musculus). Wetland type had no effect on detection, temporary emigration, or survival for any of these species. However, fecundity and population growth for all three species were affected by an interaction of season and wetland type, although none of these parameters was consistently superior in either habitat type. Estimated abundance of SMHM and Mus was similar in both wetland types, whereas WHM were more abundant in managed wetlands. Salt marsh harvest mice also showed no affinity for any microhabitat characteristics associated with tidal wetlands. Managed wetlands in Suisun Marsh support SMHM and Mus equally, and abundances of WHM were greater than in tidal wetlands, suggesting managed wetlands may be superior in terms of supporting native rodents. As climate change and sea level rise are predicted to threaten coastal marshes, these results suggest the recovery strategy for SMHM could incorporate managed wetlands. [ABSTRACT FROM AUTHOR]