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  Subjects -> GEOGRAPHY (Total: 493 journals)
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San Francisco Estuary and Watershed Science
Journal Prestige (SJR): 0.835
Citation Impact (citeScore): 2
Number of Followers: 0  

  This is an Open Access Journal Open Access journal
ISSN (Print) 1546-2366
Published by eScholarship Homepage  [73 journals]
  • I’m not that Shallow – Different Zooplankton Abundance but Similar
           Community Composition Between Habitats in the San Francisco Estuary

    • Abstract: 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 prior to restoration. During the springs of 2017-2019, 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...
      PubDate: Tue, 11 Oct 2022 00:00:00 +000
  • Wakasagi in the San Francisco Bay–Delta Watershed: Comparative Trends in
           Distribution and Life-History Traits with Native Delta Smelt

    • Abstract: Intentional introductions of non-native fishes can have severe consequences on native communities. Wakasagi (Hypomesus nipponensis, referred to as Japanese Pond Smelt) are native to Japan and were once separated from their non-native congener the endangered Delta Smelt (Hypomesus transpacificus) of the San Francisco Estuary (hereon ‘estuary’) of California (CA). Wakasagi were introduced into CA reservoirs in the 20th century as forage fish. Wakasagi have since expanded their distribution downstream to the estuary, but less is known about Wakasagi’s current distribution status and biology in the estuary, and negative influences on Delta Smelt. In this study, we took a comparative approach by synthesizing long-term field monitoring surveys, modeling environmental associations, and quantifying phenology, growth, and diets of Wakasagi and Delta Smelt to describe abundance and range, trends of co-occurrence, and shared ecological roles between smelt species. We found Wakasagi in greatest...
      PubDate: Tue, 11 Oct 2022 00:00:00 +000
  • A Framework for Evaluating the Effects of Reduced Spatial or Temporal
           Monitoring Effort

    • Abstract: Monitoring in the San Francisco Estuary has fluctuated in sampling effort over time with changes to resources, objectives, and unforeseen events. I designed an approach to evaluate how reduced sampling would alter our ability to describe the status and trends of key species. This approach can evaluate the sensitivity of the estuary monitoring program to disruptions in sampling and whether sampling effort could be reduced without compromising the information provided by these surveys. I simulated reduced sampling on top of the historical data record (1985 – 2018) by selectively removing data and evaluating the impact on model inference. The same model structure is fit to the full dataset and several reduced datasets representing simulations of reduced sampling effort. Model predictions from reduced models are then compared to those from the full model to evaluate how reduced sampling may have affected our ability to detect key patterns in the data. In a case study, I applied this...
      PubDate: Tue, 11 Oct 2022 00:00:00 +000
  • Habitat-Specific Foraging by Striped Bass (Morone saxatilis) in the San
           Francisco Estuary, California: Implications for Tidal Restoration

    • Abstract: Non-native predatory fish strongly impact aquatic communities, and their impacts can be exacerbated by anthropogenic habitat alterations. Loss of natural habitat and restoration actions reversing habitat loss can modify relationships between non-native predators and prey. Predicting how these relationships will change is often difficult because insufficient information exists on the habitat-specific feeding ecology of non-native predators. To address this information gap, we examined diets of non-native Striped Bass (Morone saxatilis; 63 to 671 mm standard length; estimated age 1-5 yrs) in the San Francisco Estuary during spring and summer in three habitat types – marsh, shoal, and channel – with the marsh habitat type serving as a model for ongoing and future restoration. Based on a prey-specific index of relative importance, Striped Bass diets were dominated by macroinvertebrates in spring and summer (amphipods in spring, decapods and isopods in summer). In spring,...
      PubDate: Tue, 11 Oct 2022 00:00:00 +000
  • Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) North of
           the San Francisco Estuary

    • Abstract: Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the SFE at the southern edge of their distribution. However, populations also exist in other estuaries along the coast, which are far less described despite their potential importance in a metapopulation. We surveyed Longfin Smelt populations along the northern California coast for larval recruitment. We conducted surveys in 2019 and 2020 to (1) identify estuaries north of SFE where spawning occurs, and (2) evaluate how habitat features (e.g., salinity, temperature, dissolved oxygen, turbidity) influenced Longfin Smelt larvae abundance. We detected larvae in four of 16 estuaries we surveyed, and all were large estuaries north of Cape Mendocino. No larvae were detected in eight coastal estuaries in closer proximity to the SFE. Larvae catch probability increased...
      PubDate: Tue, 11 Oct 2022 00:00:00 +000
  • Nutrient and Trace Element Contributions from Drained Islands in the
           Sacramento–San Joaquin Delta, California

    • Abstract: 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. These data were used to calculate island-level fluxes and then upscaled to estimate Delta-wide contributions from island drains. Based on these results, we present (1) new estimates of gross and net nutrient and trace element fluxes from Delta island drains, and (2) concomitant...
      PubDate: Mon, 20 Jun 2022 00:00:00 +000
  • Considerations for the Development of a Juvenile Production Estimate for
           Central Valley Spring-Run Chinook Salmon

    • Abstract: 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. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers,...
      PubDate: Mon, 20 Jun 2022 00:00:00 +000
  • Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco

    • Abstract: Gill-net size selectivity for fifteen 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. Selectivity curves are provided for each species to inform researchers about population characteristics of fishes sampled with similar gill nets.
      PubDate: Mon, 20 Jun 2022 00:00:00 +000
  • Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A

    • Abstract: Climate change is intensifying the effects of multiple interacting stressors on aquatic ecosystems, particularly in estuaries. 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). Based on our review, we found that the estuary is experiencing shifting baseline environmental conditions, amplification of extremes, and restructuring of physical habitats and biological communities. We present priority topics for research and monitoring, and a conceptual model of how the estuary currently functions in relation to climate variables. In addition, we discuss four tools for management...
      PubDate: Mon, 20 Jun 2022 00:00:00 +000
  • Machine Learning Forecasts to Reduce Risk of Entrainment Loss of
           Endangered Salmonids at Large-Scale Water Diversions in the
           Sacramento–San Joaquin Delta, California

    • Abstract: 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. We use a quantile regression forest approach to create a risk forecasting tool, which can inform adjustments of diversions based on near real-time predictions. Models were trained using historical entrainment data (Water Years 1999–2019) for Sacramento River winter-run Chinook Salmon or Central Valley Steelhead and a suite of environmental and water operations metrics. A range of models was developed; their performance was evaluated by comparison of a quantile loss...
      PubDate: Mon, 20 Jun 2022 00:00:00 +000
  • Multi-Biomarker Analysis for Identifying Organic Matter Sources in Small
           Mountainous River Watersheds: A Case Study of the Yuba River Watershed

    • Abstract: Organic matter in soils and sediments derives from a mixture of biological origins, often making it difficult to determine inputs from individual sources. Complicating the determination of source inputs to soil and sedimentary organic matter (OM) is the fact that physical and microbial processes have likely modified the initial composition of these sources. This study focused on identifying the composition of watershed-derived OM to better understand inputs to inland waters and improve our ability to resolve between terrigenous and aquatic sources in downstream systems, such as estuaries and coasts. We surveyed OM sources from the Yuba River watershed in northern California to identify specific biomarkers that represent aquatic and terrigenous OM sources. Multiple classes of organic proxies—including sterols, fatty acids (FA), lignin phenols and stable carbon and nitrogen isotope values (δ13C, δ15N)—were measured in soils, vegetation, charcoal, and freshwater...
      PubDate: Sun, 6 Mar 2022 00:00:00 +0000
  • Investigation of Molecular Pathogen Screening Assays for Use in Delta

    • Abstract: 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...
      PubDate: Sun, 6 Mar 2022 00:00:00 +0000
  • Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the
           San Francisco Estuary

    • Abstract: Fish monitoring gears rarely capture all available fish, an inherent bias in monitoring programs referred to as catchability. Catchability is a source of bias that can be affected by numerous aspects of gear deployment (e.g., deployment speed, mesh size, and avoidance behavior). Thus, care must be taken when multiple surveys—especially those using different sampling methods—are combined to answer spatio-temporal questions about population and community dynamics. We assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary: the Bay Study Otter Trawl (BSOT), the Bay Study Midwater Trawl (BSMT), the Fall Midwater Trawl (FMWT), and the Suisun Marsh Otter Trawl (SMOT). We used generalized additive models with a spatio-temporal smoother and survey as a fixed effect to predict gear-specific estimates of catch for 45 different fish species within large and small size classes. We used estimates of the fixed effect coefficients...
      PubDate: Sun, 6 Mar 2022 00:00:00 +0000
  • Variation in Juvenile Salmon Growth Opportunities Across a Shifting
           Habitat Mosaic

    • Abstract: Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced habitat loss, previous work using otolith reconstructions has revealed that some juvenile salmon continue to successfully rear for extended periods in the Delta. However, the extent to which the Delta functions to promote salmon growth relative to other habitats remains unknown. In this study, we integrated otolith microstructure (daily increment count and width) and strontium isotope (87Sr/86Sr) records to fill this critical knowledge gap by comparing the growth of natural-origin fall-run Chinook Salmon from the American River that reared in the Delta with those that remained in their natal stream. Using generalized additive models,...
      PubDate: Sun, 6 Mar 2022 00:00:00 +0000
  • Counting the Parts to Understand the Whole: Rethinking Monitoring of
           Steelhead in California’s Central Valley

    • Abstract: Steelhead (Oncorhynchus mykiss expressing an anadromous life history) in the Sacramento and San Joaquin rivers and their tributaries in California’s Central Valley (CCV) belong to a Distinct Population Segment (DPS) that is listed as threatened under the US Endangered Species Act. Although contemporary management and recovery plans include numerous planned and ongoing efforts seeking to aid in DPS recovery—such as gravel augmentation, manipulation of spring flows, and restoration of rearing and spawning habitat—a paucity of data precludes the possibility of evaluating the effect of these actions on populations of Steelhead in CCV streams. Knowledge gaps relating to historic and current abundance, population-specific ratios of resident and anadromous life-history expression, and the influence of hatchery-reared fish remain largely unaddressed. This is partly a result of aspects of Steelhead biology that make them difficult to monitor, including the multitude of factors...
      PubDate: Sun, 6 Mar 2022 00:00:00 +0000
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