SFEWS Vol. 20, Issue 2 | June 2022
#ChinookSalmon #SacramentoSplittail #tidalmarsh #floodplain #openwater #drought #flood #juvenileproductionestimate #JPE #lifehistory #raceidentification #springrun #SacramentoRiver #CADelta #quantile #regressionforest #Steelhead #machinelearning #entrainmentloss #SanFrancisco #estuary #SFE #BayDelta #gillnet #gearselectivity #Drainage #waterquality #agriculturaldrainage #returnflow #diversions #Delta #island #groundwater #nitrogen #phosphorous #metals
Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon
Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley.
Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California
Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta.
Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary
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 them were estimated indirectly using generalized linear modeling and maximum likelihood.
Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California
Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018.
Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review ample header
In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems (anadromous Chinook Salmon, Oncorhynchus tshawytscha and estuarine resident Sacramento Splittail, Pogonichthys macrolepidotus).
Volume 17, Issue 4, 2019
Sixteen years ago, in October 2003, San Francisco Estuary and Watershed Science (SFEWS) published its first article. An anniversary like this is a good time to remind ourselves of our history, and to ask if the journal is living up to the goals we set in 2003. And if so, are those goals consistent with today’s needs? In 2004, CDL’s eScholarship Publishing Group counted an average of 254 requests per month for SFEWS online articles. In 2010, that increased to 1,232 requests per month, and in 2014 to 1,764 per month. In the first 10 months of 2019, 4,420 articles were requested per month. Downloads have been consistently 35% to 40% of requests. Taking data from 2014 through 2017, the search engine Scopus’ CiteScore for SFEWS increased from 0.32 to 1.64; its rank is 82nd of 203 journals in the Water Science and Technology category for 2018, a remarkable climb from being ranked 120 of 179 in 2014. SFEWS is ranked fifth among 53 open access journals in the aquatic sciences, according to the Science Journal Ranking index; and in the top 25% among all 218 aquatic science journals ranked by that index. Thus, SFEWS has grown from an outlet designed to expand access to regional science to a well-respected scientific journal in its own right. Our look back shows that SFEWS has probably grown beyond our original expectations in size, influence, and stature.
Policy and Program Analysis
Review of and Recommendations for Monitoring Contaminants and their Effects in the San Francisco Bay−Delta
Legacy and current-use contaminants enter into and accumulate throughout the San Francisco Bay−Delta (Bay−Delta), and are present at concentrations with known effects on species important to this diverse watershed. There remains major uncertainty and a lack of focused research able to address and provide understanding of effects across multiple biological scales, despite previous and ongoing emphasis on the need for it. These needs are challenging specifically because of the established regulatory programs that often monitor on a chemical-by-chemical basis, or in which decisions are grounded in lethality-based endpoints. To best address issues of contaminants in the Bay−Delta, monitoring efforts should consider effects of environmentally relevant mixtures and sub-lethal impacts that can affect ecosystem health. These efforts need to consider the complex environment in the Bay−Delta including variable abiotic (e.g., temperature, salinity) and biotic (e.g., pathogens) factors. This calls for controlled and focused research, and the development of a multi-disciplinary contaminant monitoring and assessment program that provides information across biological scales. Information gained in this manner will contribute toward evaluating parameters that could alleviate ecologically detrimental outcomes. This review is a result of a Special Symposium convened at the University of California−Davis (UCD) on January 31, 2017 to address critical information needed on how contaminants affect the Bay−Delta. The UCD Symposium focused on new tools and approaches for assessing multiple stressor effects to freshwater and estuarine systems. Our approach is similar to the recently proposed framework laid out by the U.S. Environmental Protection Agency (USEPA) that uses weight of evidence to scale toxicological responses to chemical contaminants in a laboratory, and to guide the conservation of priority species and habitats. As such, we also aimed to recommend multiple endpoints that could be used to promote a multi-disciplinary understanding of contaminant risks in Bay−Delta while supporting management needs.
The Sacramento–San Joaquin Delta has been invaded by several species of non-native predatory fish that are presumed to be impeding native fish population recovery efforts. Since eradication of predators is unlikely, there is substantial interest in removing or altering manmade structures in the Delta that may exacerbate predation on native fish (contact points). It is presumed that these physical structures influence predator-prey dynamics, but how habitat features influence species interactions is poorly understood, and physical structures in the Delta that could be remediated to benefit native fish have not been inventoried completely. To inform future research efforts, we reviewed literature that focused on determining the effects of predator-prey interactions between fish, based on contact points that are commonly found in the Delta. We also performed a geospatial analysis to determine the extent of potential contact points in the Delta. We found that the effects of submerged aquatic vegetation (SAV) and artificial illumination are well studied and documented to influence predation in other freshwater systems worldwide. Conversely, other common structures in the Delta—such as docks, pilings, woody debris, revetment, and water diversions—did not have the same breadth of research. In the Delta, the spatial extent of the different types of contact points differed considerably. For example, 22% of the Delta water surface area is occupied by SAV, whereas docks only cover 0.44%. Our conclusion, based on both the literature review and spatial analysis, is that the effects of SAV and artificial illumination on predation warrant the most immediate future investigation in the Delta.
A Bayesian hierarchical model that integrated information about state and observation processes was used to estimate the number of adult Delta Smelt entrained into the southern Sacramento−San Joaquin Delta during water export operations by the California State Water Project and the Central Valley Project. The model hierarchy accounted for dynamic processes of transport, survival, sampling efficiency, and observation. Water export, mark−recapture, and fish facility count data informed each process. Model diagnostics and simulation testing indicated a good fit of the model, and that parameters were jointly estimable in the Bayesian hierarchical model framework. The model was limited, however, by sparse data to estimate survival and State Water Project sampling efficiency. Total December to March entrainment of adult Delta Smelt ranged from an estimated 142,488 fish in 2000 to 53 fish in 2014, and the efficiency of louvers used to divert entrained fish to fish facilities appeared to decline at high and low primary intake channel velocities. Though applied to Delta Smelt, the hierarchical modeling framework was sufficiently flexible to estimate the entrainment of other pelagic species.
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