SFEWS Vol. 20, Issue 1 | March 2021
#CentralValley #ChinookSalmon #otolithchemistry #Steelhead #monitoring #surveys #catchability #detectionefficiency #DeltaSmelt #supplementation #Ich #pathogens #organiccarbon #stablecarbon #nitrogen #inputs #YubaRiver #watersheds
Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic
Coleman et al. found that juvenile Chinook Salmon grew faster in the Delta in some years (2016), but slower in the Delta during drought conditions (2014 to 2015). Habitat that featured faster growth rates varied within and among years, suggesting the importance of maintaining a habitat mosaic for juvenile salmonids, particularly in a dynamic environment such as the California Central Valley.
Counting the Parts to Understand the Whole: Rethinking Monitoring of Steelhead in California’s Central Valley
Eschenroeder et al. argue that a reallocation of monitoring resources to better understand the interaction between resident and anadromous Steelhead would provide better data to estimate the vital rates needed to evaluate the effects of recovery actions.
Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the San Francisco Estuary
Huntsman et al. assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary. Their results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.
Investigation of Molecular Pathogen Screening Assays for Use in Delta Smelt
Gille et al. conducted 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. Although disease is not an overt cause of population decline of Delta Smelt in the San Francisco Estuary, comprehensive pathogen presence and prevalence data are lacking, and unintended transmission of pathogens can have devastating effects on populations already at-risk or on the natural ecosystem at large. Their results corroborate previous work that cultured Delta Smelt do not appear to present a high risk for pathogen transmission during population supplementation or reintroduction.
Multi-Biomarker Analysis for Identifying Organic Matter Sources in Small Mountainous River Watersheds: A Case Study of the Yuba River Watershed
Pondell and Canuel's study focused on identifying the composition of watershed-derived organic matter (OM). To better understand inputs to inland waters and improve distinguish between terrigenous and aquatic sources in downstream systems, such as estuaries and coasts, they surveyed OM sources from the Yuba River watershed in northern California to identify specific biomarkers that represent aquatic and terrigenous OM sources. Results demonstrate the utility of multi-biomarker studies for distinguishing between OM from different sources and land uses, offering new insights for biogeochemical studies in aquatic systems.
Volume 11, Issue 2, 2013
Circulation in Clifton Court Forebay (CCF) was simulated using the three-dimensional (3–D) hydrodynamic model UnTRIM. These numerical simulations were performed to provide a better understanding of circulation patterns, flow pathways, and residence time in Clifton Court Forebay in support of ongoing studies of pre-screen loss and fish facility efficiency for delta smelt (Hypomesus transpacificus) at the California State Water Project (SWP) export facilities. The 3–D hydrodynamic model of CCF was validated through comparisons to observed water surface elevations inside CCF, and comparisons to observed drifter paths and velocity measurements collected by the U.S. Geological Survey as part of this study. Flow measurements collected near the radial gates for 2 days during relatively low inflows suggest that the Hills (1988) gate equations may over-estimate inflow by as much as 39% when the CCF radial gates are only partially opened. Several alternative approaches to improve the implementation of the radial gate flows in the UnTRIM model were evaluated. The resulting model accurately predicts water surface elevations and currents inside CCF over a range of wind and operating conditions. The validated model was used to predict residence time and other transport time scales for two 21-day simulation periods, one of very low daily SWP export pumping averaging 19.3 m3 s-1 and one for moderate daily SWP export pumping averaging 66.6 m3 s-1. The average transit time, indicating the time from entering CCF to reaching the fish facility, was estimated as 9.1 days for low export conditions and 4.3 days for moderate export conditions. These transport time scale estimates may be used to inform estimates of pre-screen losses inside CCF due to predation or other causes.
- 1 supplemental PDF
Salmon Lifecycle Considerations to Guide Stream Management: Examples from California’s Central Valley
A primary goal of the Central Valley Project Improvement Act is to at least double natural production of Chinook salmon (Oncorhynchus tshawytscha), in California Central Valley (CV) streams on a sustainable basis. Achievement relies on restoration actions that involve both discharge (e.g., dam releases) and non-discharge (e.g., gravel augmentation, screening) components. Annual adult and juvenile abundance estimates for individual watersheds must be tracked to assess effectiveness of individual actions. However, to date, no substantial efforts have been taken to demonstrate success or deficiencies of their implementations. A major challenge in interpreting time series of counts at any one life stage is that they reflect the cumulative effects of both freshwater and marine factors over the full life cycle. To address this issue, we developed a conceptual framework based on ratios of the abundance of consecutive CV fall-run Chinook salmon life stages and how variation in these ratios tracks key independent variables during the freshwater portion of the life cycle. Model validation with several case studies shows that estimates of previous stage class production correlate well with estimated individuals produced in the next class, indicating that transition rates tend to vary within a constrained range, and that monitoring programs generate abundance estimates whose errors are small enough not to swamp out the underlying signal. When selected environmental parameters were added to demonstration models, abundance estimates were more closely modeled and several tested relationships between environmental drivers and life-stage transition rates proved consistent across watersheds where data were available. Results from this generalized life-stage conceptual model suggest a potential framework for tracking the success of actions meant to improve survival for a given life stage within an individual stream and for determining how successive stages respond to these changes. Though examples are provided for CV Chinook salmon, these concepts can be applied wherever migratory salmonid populations and associated environmental data are being adequately monitored.
Erratum dated 2014 June 25
Pharmaceuticals and personal care products (PPCPs) are found in surface waters worldwide. Wastewater treatment plant effluent is a major source of these contaminants. The Sacramento–San Joaquin Delta (Delta) is a unique aquatic ecosystem, a source of drinking water for over 25 million Californians, and a primary source of water for Central Valley agriculture. The sharp decline of four pelagic fish species in the Delta in the last decade is just one of several indicators that the ecosystem is severely impaired. Several wastewater treatment plants (WWTPs) discharge into the Delta, directly or through tributaries. The presence of PPCPs in the Delta has received very little attention relative to the immense effort underway to rehabilitate the ecosystem. This study determined concentrations of PPCPs in the Sacramento River in the vicinity of the Sacramento Regional Wastewater Treatment Plant using passive sampler monitoring. These data were used to estimate loads of three of the detected pharmaceuticals (carbamazepine, fluoxetine, and trimethoprim) from nine other WWTPs that discharge to the Delta. The 2-D, finite element, Resource Management Associates (RMA) Delta Model was then applied to determine the distribution that might result from these discharges. The model was run for the 2006, 2007, and 2009 water years. Results indicate that it is feasible that WWTP discharges could result in chronic presence of these pharmaceuticals at low ng L-1 levels at all 45 model output locations and, therefore, aquatic organisms within the Delta may be continually exposed to these contaminants.
- 1 supplemental PDF
We used a combination of published literature and field survey data to synthesize the available information about habitat use by delta smelt Hypomesus transpacificus, a declining native species in the San Francisco Estuary. Delta smelt habitat ranges from San Pablo and Suisun bays to their freshwater tributaries, including the Sacramento and San Joaquin rivers. In recent years, substantial numbers of delta smelt have colonized habitat in Liberty Island, a north Delta area that flooded in 1997. The species has a more upstream distribution during spawning as opposed to juvenile rearing periods. Post-larvae and juveniles tend to have a more downstream distribution during wetter years. Delta smelt are most common in low-salinity habitat (<6 psu) with high turbidities (>12 NTU) and moderate temperatures (7 °C to 25 °C). They do not appear to have strong substrate preferences, but sandy shoals are important for spawning in other osmerids. The evidence to date suggests that they generally require at least some tidal flow in their habitats. Delta smelt also occur in a wide range of channel sizes, although they seem to be rarer in small channels (<15 m wide). Nonetheless, there is some evidence that open water adjacent to habitats with long water-residence times (e.g. tidal marsh, shoal, low-order channels) may be favorable. Other desirable features of delta smelt habitat include high calanoid copepod densities and low levels of submerged aquatic vegetation (SAV) and the toxic algae Microcystis. Although enough is known to plan for large-scale pilot habitat projects, these efforts are vulnerable to several factors, most notably climate change, which will change salinity regimes and increase the occurrence of lethal temperatures. We recommend restoration of multiple geographical regions and habitats coupled with extensive monitoring and adaptive management. An overall emphasis on ecosystem processes rather than specific habitat features is also likely to be most effective for recovery of the species.