San Francisco Estuary and Watershed Science

Managing river–floodplain connectivity can be driven by environmental restoration and/or flood-risk objectives, and science programs are essential for informing projects and policies that promote both objectives. California’s Central Valley floodplains have been highly altered as the result of flow regulation, channelization, and levee construction. Much of the remaining floodplain-like habitats are within flood bypasses that are used to manage flood risk. In recent decades, the habitat value of these bypasses for native fishes has received increased attention, and in 2021 a symposium was held to share the results of over 20 years of scientific studies conducted on Central Valley floodplains and flood bypasses. The symposium sought to foster a shared understanding among scientists and managers about the current information on flood bypasses, and the remaining challenges that must be overcome to maximize benefits to native fish while managing trade-offs. This paper summarizes the symposium’s unique synthesis of the state of the science regarding benefits that native fish accrue from accessing flood bypasses, and remaining uncertainties about population-level benefits and risks when fish enter these systems. We describe a case study to demonstrate how restoration can be accomplished within the flood-bypass management context, provide examples of ongoing restoration projects in the Central Valley, and present recommendations for actions needed to manage and restore flood bypasses at a landscape-scale. Our summary identifies the need to develop a long-term vision for managing and restoring flood bypasses and floodplains throughout the valley that includes: quantifying fish population-level effects, identifying necessary funding sources to implement actions at a scale that achieves societal goals, and streamlining regulatory processes. These steps would allow the actions identified in the vision to be implemented in a transparent, consensus-driven, and timely manner.

We used acoustic telemetry to estimate survival of tagged release groups, and quantify differences between alternative hatchery release strategies. To assess whether offsite release could increase survival of hatchery fish relative to those released at the hatchery, we compare survival during emigration of hatchery fall Chinook Salmon (FCS, Oncorhynchus tshawytscha) smolts released onsite, at Coleman National Fish Hatchery (NFH), to those released at alternative offsite locations downstream in the upper Sacramento River, California. Approximately 300 fish in each release group were implanted with acoustic tags in the 3-year study during 2019, 2021, and 2022. Environmental conditions in the emigration corridor varied between study years, with extended high flows in 2019, whereas drought conditions and a flat hydrograph occurred in 2021 and 2022. Survival across years appeared to reflect environmental conditions, with higher overall survival seen in 2019. Survival differences between release sites generally showed higher cumulative survival to Knights Landing or Chipps Island for the downstream release groups, compared to the onsite releases during 2021 and 2022. This information suggests hatchery releases of FCS from Coleman NFH at downstream release sites may benefit emigration survival during years of drought and sub-optimal in-river conditions, compared to standard onsite releases. Hatchery managers can use information from this study to diversify the portfolio of release strategies, which may be useful to buffer against extreme variations of adult abundance by spreading risks across space and time. Ultimately, offsite releases may be a useful tool for adaptive management of these culturally, ecologically, and economically important salmon populations.

The survival of juvenile Chinook Salmon (Oncorhynchus tshawytscha) depends on the specific migration route they take through the Sacramento–San Joaquin Delta. Factors such as flow magnitude, flow direction, and distribution of fish across the channel significantly affect the likelihood of their entering routes with lower survival probabilities. Management strategies to mitigate the entry of endangered winter-run and threatened spring-run Chinook Salmon into the interior Delta—particularly through Georgiana Slough—involve flow regulation and the installation of a bioacoustic fish fence. Monitoring the effectiveness of these measures has primarily relied on acoustically-tagged, juvenile, hatchery-reared, late-fall-run Chinook Salmon, which are easier to obtain and can accommodate larger tags compared to other runs. Previous studies explored how flow dynamics affect routing probabilities of late-fall-run Chinook Salmon, but there is a lack of understanding about how routing probabilities vary among runs. We leveraged data from 15 previous studies comprising 3,004 acoustically-tagged fish across all four runs, over a 12-year period, to assess the effects of run on routing probability into Georgiana Slough, while accounting for variation in flow dynamics. We employed logistic regression to model the influence of tidal flow metrics, time of day (day and night), and run type on the probability of juvenile Chinook Salmon being routed into Georgiana Slough. Our analysis revealed that reverse flow during incoming tides influenced the routing probabilities of all runs. An increased proportion of flow into Georgiana Slough, meant an increased probability for all runs to be routed into Georgiana Slough. Late-fall-run Chinook Salmon also showed a greater probability of routing into Georgiana Slough during the night than during the day, whereas the opposite was true for other runs. These differences in routing probability affect our understanding of how management actions intended to reduce routing into Georgiana Slough may differentially affect the four runs of Chinook Salmon in the Sacramento River.

Current ecological conditions in the San Francisco Estuary are considered inhospitable to many native estuarine species, and have placed the endemic Delta Smelt (Hypomesus transpacificus) at serious risk. Programmatic monitoring regimes conducted by government agencies are insufficient for associating Delta Smelt occurrence with relevant habitat attributes, which limits inference about the relationships between putative habitat, restoration activities, and population response. Indirect observation of macro-organisms via detection of environmental DNA (eDNA) has proved a compelling alternative monitoring approach, particularly for rare and/or protected species. Yet, factors that influence eDNA detection in estuarine habitats remain poorly characterized, which hinders refinement of sampling methods. This study employed a fixed sampling array to explore how tidal phases affect the detection of Delta Smelt eDNA. Our primary objective was to estimate the effects of covariate metrics on concentration of eDNA (calculated as ln[eDNA]) observed in the tidal environment. Secondary objectives included comparing the effect of distance on eDNA concentration in the tidal system vs. a unidirectional system and estimating how time since species absence affects observed eDNA concentration. Model predictors that consistently affected eDNA concentration were distance from source, eddy diffusivity, time since species absence, tidal direction, and species. Distance had a consistently negative effect on eDNA concentration across both systems, though non-detections were more frequent in the tidal system than expected in a unidirectional one. Environmental DNA detections decreased over time, which suggests that positive eDNA detections from estuarine water sampling are more likely to co-occur contemporaneously with the actual presence of individuals. These findings improve the capacity to design sampling strategies that will detect target species within an estimated probability, if individuals are present within a specified distance. Enhanced detections using eDNA sampling approaches would refine determinations of if and when Delta Smelt are present at a location, which in turn lessens known information gaps related to species occurrence and distribution.

The release of hatchery-reared fish into the natural environment for conservation purposes may have unintended consequences for wild fish populations and the larger ecosystem. In situ enclosures are a tool that can be used to study cultured fish under natural conditions to help mitigate these risks or to acclimate fish to the surrounding environment during soft release. Despite widespread utility, few resources provide direction on material choice and enclosure design to conserve non-commercial and imperiled fish species that may have unique physiology and needs. Here, we designed, created, and tested an enclosure for the endangered Delta Smelt (Hypomesus transpacificus), an osmerid native to the San Francisco Estuary (estuary). We first performed hydraulic modeling and evaluated permeability to prey items by measuring energy dissipation and flow deflection of candidate screen materials in a flume. The final enclosure design was a cylinder made out of stainless-steel wire mesh, with 60% openness that measured 1.0 m in diameter and 1.3 m tall. We then investigated survival, growth, and feeding of cultured Delta Smelt in the enclosure in three 1-month-long deployments in an experimental pond. Fish survival was moderate to high (50% to 93%), and we observed that Delta Smelt in the enclosures spontaneously converted to live, natural food, which suggests that cultured fish will be able to forage when released into the estuary. We hope that the steps we have outlined and the final enclosure design will be instrumental in supplementing Delta Smelt and conserving other at-risk fish species in the future.

Although formalin is commonly used as a preserving reagent for tissue specimens, the fixation process itself damages DNA, which can be detrimental to most downstream genetic analyses. It may still be possible to confirm species identification from archived specimens by targeting short, species-specific genic regions. In this study we genetically verified maternal mitochondrial lineage from 150 hatchery larval Delta Smelt (Hypomesus transpacificus) that were preserved in 10% neutral, buffered formalin and Rose Bengal at room temperature (20–22 °C) for 611 days, 732 days, and 928 days. We targeted a region of the mitochondrial cytochrome b (Cyt-b) gene using a quantitative PCR (qPCR) assay designed to specifically amplify Delta Smelt environmental DNA (eDNA). Because mitochondrial genetic markers used for species identification are generally maternally inherited, detecting hybridization is not possible using species-specific mitochondrial markers if among-species hybrids are present. Because Delta Smelt can hybridize with non-native Wakasagi Smelt (Hypomesus nipponensis), we assumed in this study the method detected maternal lineage. Maternal mitochondrial lineage was confirmed in 100% of our 150 Delta Smelt samples analyzed, although the strength of detection appeared to decline over time. We posit that the short DNA target size (84 base pairs) of the Delta Smelt-specific qPCR assay allowed for successful identification, and we confirmed this by Sanger sequencing with the qPCR assay forward and reverse primers. Our results may be broadly applicable because formalin remains a commonly used fixative in the preservation of fish, reptiles, amphibians, and various invertebrate taxa. Additional testing with both Sanger- and Illumina-based sequencing methods on a subset of the larval extracts did not successfully produce positive identification.