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.
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.
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.
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.
