Pub Date : 2022-10-14DOI: 10.15447/sfews.2022v20iss3art3
C. Brennan, Jason L. Hassrick, A. Kalmbach, D. Cox, Megan C. Sabal, Ramona Zeno, L. Grimaldo, S. Acuña
Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (the SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the estuary 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 meta-population. 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 the 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 with turbidity and decreased with salinity with no significant influence of temperature and dissolved oxygen. In the wet winter of 2019, we observed lower densities of larvae in Humboldt Bay and the Eel River, and detected no Longfin Smelt in the Klamath and Mad Rivers; in the dry winter of 2020, we detected larvae in two additional estuaries. Possibly elevated freshwater outflow in 2019 increased transport rates to the sea, resulting in the observed low larval recruitment. Our results suggest that, while populations of Longfin Smelt exist in large estuaries north of Cape Mendocino, coastal estuaries in proximity to the SFE were either under-sampled or are not permanently inhabited by Longfin Smelt. This suggests that the threatened estuary Longfin Smelt population may lack the resiliency afforded by meta-populations and advocates for increased monitoring over a range of hydrologic conditions and improving detection probabilities for future assessments of gene flow between populations.
{"title":"Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) north of the San Francisco Estuary","authors":"C. Brennan, Jason L. Hassrick, A. Kalmbach, D. Cox, Megan C. Sabal, Ramona Zeno, L. Grimaldo, S. Acuña","doi":"10.15447/sfews.2022v20iss3art3","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss3art3","url":null,"abstract":"Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (the SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the estuary 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 meta-population. 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 the 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 with turbidity and decreased with salinity with no significant influence of temperature and dissolved oxygen. In the wet winter of 2019, we observed lower densities of larvae in Humboldt Bay and the Eel River, and detected no Longfin Smelt in the Klamath and Mad Rivers; in the dry winter of 2020, we detected larvae in two additional estuaries. Possibly elevated freshwater outflow in 2019 increased transport rates to the sea, resulting in the observed low larval recruitment. Our results suggest that, while populations of Longfin Smelt exist in large estuaries north of Cape Mendocino, coastal estuaries in proximity to the SFE were either under-sampled or are not permanently inhabited by Longfin Smelt. This suggests that the threatened estuary Longfin Smelt population may lack the resiliency afforded by meta-populations and advocates for increased monitoring over a range of hydrologic conditions and improving detection probabilities for future assessments of gene flow between populations.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43520706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-10-14DOI: 10.15447/sfews.2022v20iss3art4
M. Young, F. Feyrer, Collin D. Smith, D. Valentine
Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restoration actions that reverse 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; 63–671 mm standard length; estimated age 1–5 y) 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, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin (Cottus asper) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~ 40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly because of the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.
{"title":"Habitat-Specific Foraging by Striped Bass (Morone saxatilis) in the San Francisco Estuary, California: Implications for Tidal Restoration","authors":"M. Young, F. Feyrer, Collin D. Smith, D. Valentine","doi":"10.15447/sfews.2022v20iss3art4","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss3art4","url":null,"abstract":"Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restoration actions that reverse 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; 63–671 mm standard length; estimated age 1–5 y) 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, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin (Cottus asper) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~ 40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly because of the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45555271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-10-14DOI: 10.15447/sfews.2022v20iss3art2
B. Davis, Jesse Adams, Levi S. Lewis, J. Hobbs, Naoaki Ikemiyagi, C. Johnston, L. Mitchell, Anjali W Shakya, B. Schreier
Intentional introductions of non-native fishes can severely affect 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. Wakasagi were introduced into California 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, 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 abundance in the upper watershed below source reservoirs, and in the northern regions of the estuary with the most co-occurrence with Delta Smelt; however, their range extends to western regions of the estuary, and we found evidence of an established population that annually spawns and rears in the estuary. We found these smelt species have similar ecological roles demonstrated by overlaps in habitat use (e.g., an association with higher turbidities and higher outflow), phenology, growth, and diets. Despite similarities, earlier hatching and rearing of Wakasagi during cooler months and reduced growth during warmer drought years suggest this species is unlike typical non-natives (e.g., Centrarchids), and they exhibit a similar sensitivity to environmental variability as Delta Smelt. This sensitivity may be why Wakasagi abundance remains relatively low in the estuary.
{"title":"Wakasagi in the San Francisco Bay Delta Watershed: Comparative Trends in Distribution and Life-History Traits with Native Delta Smelt","authors":"B. Davis, Jesse Adams, Levi S. Lewis, J. Hobbs, Naoaki Ikemiyagi, C. Johnston, L. Mitchell, Anjali W Shakya, B. Schreier","doi":"10.15447/sfews.2022v20iss3art2","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss3art2","url":null,"abstract":"Intentional introductions of non-native fishes can severely affect 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. Wakasagi were introduced into California 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, 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 abundance in the upper watershed below source reservoirs, and in the northern regions of the estuary with the most co-occurrence with Delta Smelt; however, their range extends to western regions of the estuary, and we found evidence of an established population that annually spawns and rears in the estuary. We found these smelt species have similar ecological roles demonstrated by overlaps in habitat use (e.g., an association with higher turbidities and higher outflow), phenology, growth, and diets. Despite similarities, earlier hatching and rearing of Wakasagi during cooler months and reduced growth during warmer drought years suggest this species is unlike typical non-natives (e.g., Centrarchids), and they exhibit a similar sensitivity to environmental variability as Delta Smelt. This sensitivity may be why Wakasagi abundance remains relatively low in the estuary.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43344064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-24DOI: 10.15447/sfews.2022v20iss2art5
C. Richardson, Joseph K. Fackrell, T. Kraus, M. Young, A. Paytan
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 N stable isotope data to improve our understanding of island N cycling. Over 60% of nearly all island drainage gross nutrient and trace element loads occurred in winter and spring. Upscaled island drainage net annual total nitrogen (TN), total dissolved nitrogen (TDN), and NH4+ loads comprised an estimated 9%, 7%, and 4%, respectively, of annual inputs to this system in 2018, before the SRWTP upgrade. Under a post-upgrade scenario, we estimated net annual island drainage TDN contributions to increase to 11% and NH4+ contributions to 45% of total Delta inputs as the SRWTP NH4+ load diminished to near zero. Our results suggest that island drainage is a measurable N source that has likely become increasingly important now that the SRWTP upgrade is complete. With over 200 potential active outfalls, these inputs may affect aquatic biogeochemical cycling in many regions of the Delta, especially in areas with long residence times.
{"title":"Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California","authors":"C. Richardson, Joseph K. Fackrell, T. Kraus, M. Young, A. Paytan","doi":"10.15447/sfews.2022v20iss2art5","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss2art5","url":null,"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 N stable isotope data to improve our understanding of island N cycling. Over 60% of nearly all island drainage gross nutrient and trace element loads occurred in winter and spring. Upscaled island drainage net annual total nitrogen (TN), total dissolved nitrogen (TDN), and NH4+ loads comprised an estimated 9%, 7%, and 4%, respectively, of annual inputs to this system in 2018, before the SRWTP upgrade. Under a post-upgrade scenario, we estimated net annual island drainage TDN contributions to increase to 11% and NH4+ contributions to 45% of total Delta inputs as the SRWTP NH4+ load diminished to near zero. Our results suggest that island drainage is a measurable N source that has likely become increasingly important now that the SRWTP upgrade is complete. With over 200 potential active outfalls, these inputs may affect aquatic biogeochemical cycling in many regions of the Delta, especially in areas with long residence times.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44936845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-24DOI: 10.15447/sfews.2022v20iss2art2
P. Nelson, M. Baerwald, O. Burgess, Eva Bush, Alison L. Collins, F. Cordoleani, Henry DeBey, D. Gille, Pascale A L Goertler, Brett N. Harvey, Rachel Johnson, J. Kindopp, Erica M. Meyers, Jeremy J. Notch, C. Phillis, G. Singer, Ted R. Sommer
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, and scientists to review some of the key aspects of spring-run biology, examine the management and conservation importance of a JPE, identify knowledge gaps, introduce new tools, and discuss alternative approaches to forecasting the number of spring run emigrating from the Sacramento River drainage and into the Delta. This paper summarizes the spring-run biology, monitoring, and emergent methods for assessment considered at the workshop, as well as the guiding concepts identified by workshop participants necessary to develop a JPE for spring-run Chinook Salmon.
{"title":"Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon","authors":"P. Nelson, M. Baerwald, O. Burgess, Eva Bush, Alison L. Collins, F. Cordoleani, Henry DeBey, D. Gille, Pascale A L Goertler, Brett N. Harvey, Rachel Johnson, J. Kindopp, Erica M. Meyers, Jeremy J. Notch, C. Phillis, G. Singer, Ted R. Sommer","doi":"10.15447/sfews.2022v20iss2art2","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss2art2","url":null,"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, and scientists to review some of the key aspects of spring-run biology, examine the management and conservation importance of a JPE, identify knowledge gaps, introduce new tools, and discuss alternative approaches to forecasting the number of spring run emigrating from the Sacramento River drainage and into the Delta. This paper summarizes the spring-run biology, monitoring, and emergent methods for assessment considered at the workshop, as well as the guiding concepts identified by workshop participants necessary to develop a JPE for spring-run Chinook Salmon.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44638853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-24DOI: 10.15447/sfews.2022v20iss2art3
M. Tillotson, Jason L. Hassrick, Alison L. Collins, C. Phillis
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 metric. The models were validated through examination of partial dependence plots, cross-validation procedures, and further evaluated through WY 2019 pilot testing, which integrated real-world uncertainty in environmental parameters into model predictions. For both species, the strongest predictor of loss was the previous week’s entrainment loss. In addition, risk increased with higher water exports and more negative Old and Middle Rivers (OMR) flows. Point estimates of loss were modestly correlated with observations (R2 0.4 to 0.6), but the use of a quantile regression approach provided reliable prediction intervals. For both species, the predicted 75th quantile appears to be a robust and conservative estimator of entrainment risk, with overprediction occurring in fewer than 20% of cases. This quantile balances the magnitude of over- and under-prediction and results in a low probability (< 5% of predictions) of unexpected high-take events. These models, and the web-based application through which they are made accessible to non-technical users, can provide a useful and complementary approach to the current system of managing entrainment risk.
{"title":"Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California","authors":"M. Tillotson, Jason L. Hassrick, Alison L. Collins, C. Phillis","doi":"10.15447/sfews.2022v20iss2art3","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss2art3","url":null,"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 metric. The models were validated through examination of partial dependence plots, cross-validation procedures, and further evaluated through WY 2019 pilot testing, which integrated real-world uncertainty in environmental parameters into model predictions. For both species, the strongest predictor of loss was the previous week’s entrainment loss. In addition, risk increased with higher water exports and more negative Old and Middle Rivers (OMR) flows. Point estimates of loss were modestly correlated with observations (R2 0.4 to 0.6), but the use of a quantile regression approach provided reliable prediction intervals. For both species, the predicted 75th quantile appears to be a robust and conservative estimator of entrainment risk, with overprediction occurring in fewer than 20% of cases. This quantile balances the magnitude of over- and under-prediction and results in a low probability (< 5% of predictions) of unexpected high-take events. These models, and the web-based application through which they are made accessible to non-technical users, can provide a useful and complementary approach to the current system of managing entrainment risk.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44870044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-24DOI: 10.15447/sfews.2022v20iss2art1
Bruce Herbold, Eva Bush, G. Castillo, Denise D. Colombano, R. Hartman, P. Lehman, B. Mahardja, Ted R. Sommer
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 of climate change effects: regulatory, water infrastructure, habitat development, and biological measures. We conclude that adapting to climate change requires fundamental changes in management.
{"title":"Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review","authors":"Bruce Herbold, Eva Bush, G. Castillo, Denise D. Colombano, R. Hartman, P. Lehman, B. Mahardja, Ted R. Sommer","doi":"10.15447/sfews.2022v20iss2art1","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss2art1","url":null,"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 of climate change effects: regulatory, water infrastructure, habitat development, and biological measures. We conclude that adapting to climate change requires fundamental changes in management.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47143839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-06-24DOI: 10.15447/sfews.2022v20iss2art4
Marissa Wulff, F. Feyrer, M. Young
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.
{"title":"Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary","authors":"Marissa Wulff, F. Feyrer, M. Young","doi":"10.15447/sfews.2022v20iss2art4","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss2art4","url":null,"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.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41364442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-03-17DOI: 10.15447/sfews.2022v20iss20art1
Laura Coleman, Rachel C. Johnson, F. Cordoleani, C. Phillis, A. Sturrock
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, we compared daily otolith growth rates among rearing habitats (Delta vs. American River) and years (2014 to 2018), encompassing a range of hydrologic conditions. We 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). The 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. Linking otolith chemistry with daily growth increments provides a valuable approach to explore the mechanisms governing interannual variability in growth across habitat types, and a useful tool to quantify the effects of large-scale restoration efforts on native fishes.
{"title":"Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic","authors":"Laura Coleman, Rachel C. Johnson, F. Cordoleani, C. Phillis, A. Sturrock","doi":"10.15447/sfews.2022v20iss20art1","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss20art1","url":null,"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, we compared daily otolith growth rates among rearing habitats (Delta vs. American River) and years (2014 to 2018), encompassing a range of hydrologic conditions. We 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). The 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. Linking otolith chemistry with daily growth increments provides a valuable approach to explore the mechanisms governing interannual variability in growth across habitat types, and a useful tool to quantify the effects of large-scale restoration efforts on native fishes.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43788683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-03-17DOI: 10.15447/sfews.2022v20iss20art5
C. Pondell, E. Canuel
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 plankton to characterize representative source endmembers. Sterols—including 27-nor-24-cholesta-5,22-dien-3β-ol, cholesta-5,22-dien-3β-ol, 24-methylcholesta-5,22-dien-3β-ol and cholesta-5-en-3β-ol, and positive δ15N values—were associated with aquatic OM (plankton, suspended particulate OM), whereas lignin phenols, long chain FA, and diacids characterized terrigenous sources (soils, charcoal, vegetation). Trends in organic carbon and biomarker signatures in soil samples showed a response to environmental disturbance (i.e., mining, agriculture) through an inverse relationship between OM content and land use. Results from this study 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.
{"title":"Multi-Biomarker Analysis for Identifying Organic Matter Sources in Small Mountainous River Watersheds: A Case Study of the Yuba River Watershed","authors":"C. Pondell, E. Canuel","doi":"10.15447/sfews.2022v20iss20art5","DOIUrl":"https://doi.org/10.15447/sfews.2022v20iss20art5","url":null,"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 plankton to characterize representative source endmembers. Sterols—including 27-nor-24-cholesta-5,22-dien-3β-ol, cholesta-5,22-dien-3β-ol, 24-methylcholesta-5,22-dien-3β-ol and cholesta-5-en-3β-ol, and positive δ15N values—were associated with aquatic OM (plankton, suspended particulate OM), whereas lignin phenols, long chain FA, and diacids characterized terrigenous sources (soils, charcoal, vegetation). Trends in organic carbon and biomarker signatures in soil samples showed a response to environmental disturbance (i.e., mining, agriculture) through an inverse relationship between OM content and land use. Results from this study 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.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44401519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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