2025 IEP Workshop Poster Exhibits

Abstract

The U.S. Geological Survey has been collecting continuous data in the Sacramento-San Joaquin Delta (Delta) for decades. The network has expanded from several experimental stations in the 1970s and 1980s to a robust and integrated monitoring network. Today more than 40 stations are collecting a range of water-level, discharge, and water-quality data that support critical real-time water management decisions as well as in-depth analyses. Our group collaborates with stakeholders to increase the power of the data being collected across the monitoring network. The data are transformed into information in a variety of ways, including constituent mapping, salmon out-migration survival studies, interdisciplinary tidal-marsh function studies, and hydrodynamic model calibration and validation.

Long-term datasets in conjunction with modelling efforts and process-based studies provide insight into the impacts that various habitat restoration and water management actions have had on circulation and mixing in the Delta. More changes are proposed for the future that will directly impact the basic hydrodynamic processes at work in the Delta. These long-term monitoring data provide a framework for assessing the impacts of proposed actions. Moreover, as they are integrated with additional data streams, such as biological monitoring, scientists can gain insight into the impacts that physical and chemical processes have on the distribution of native and non-native species in the Delta.

Authors

• Elise Shea*^†, U.S. Geological Survey, eshea@usgs.gov
• Anna Conlen^*, U.S. Geological Survey, aconlen@usgs.gov
• Lex Thomas, U.S. Geological Survey, athomas@usgs.gov

*Presenting authors, ^†Early Career Award candidate

Abstract

The U.S. Geological Survey has been collecting suspended-sediment data in the Sacramento-San Joaquin Delta (Delta) and San Francisco Bay for decades. The network has expanded from several experimental stations in the 1990s to a robust and integrated monitoring network. Today, more than 25 stations are reporting suspended-sediment data based on turbidity surrogate models. Our group collaborates with stakeholders to increase the power of the data being collected across the monitoring network. The data are transformed into information in a variety of ways, including constituent mapping, interdisciplinary tidal-marsh function studies, and model calibration and validation.

Long-term datasets in conjunction with modelling efforts and process-based studies provide insight into the impacts that various habitat restoration and water management actions have had on circulation and mixing in the Delta. More changes are proposed for the future that will directly impact the basic hydrodynamic processes at work in the Delta. These long-term monitoring data provide a framework for assessing the impacts of proposed actions. Moreover, as they are integrated with additional data streams, such as biological monitoring, scientists can gain insight into the impacts that physical and chemical processes have on the distribution of native and non-native species in the Delta.

Authors

• Emma Walker*^†, U.S. Geological Survey
• Joseph Hatfield^*, U.S. Geological Survey
• Bryan Gopez, U.S. Geological Survey, bgopez@usgs.gov

*Presenting authors, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

Twelve of the top 20 largest wildfires in California history have occurred since 2018, burning more than 5.2 million acres mostly in northern California. This recent surge in catastrophic wildfires has increased forest regeneration efforts as well, and the use of herbicides to ensure seedling survival has increased at a similar scale. Data from the California Department of Pesticide Regulation shows that several herbicides are applied in commercial timberland operations and the most heavily used are glyphosate, hexazinone, imazapyr, oxyfluorfen, and triclopyr. Application of these herbicides increases substantially in the post-fire environment. For example, pesticide use after the North Complex fire, which burned significant portions of the Feather River watershed in 2020, increased more than 30-fold by 2022. An increase of similar magnitude occurred after the Carr fire, which burned more than 230,000 acres in the Sacramento River watershed in 2018. Water samples collected as far downstream as the Sacramento-San Joaquin Delta have shown increased frequency of detection and concentrations of post-fire herbicides in the years following major wildfires.

The effects of herbicides used in post-fire environments are not well understood or well regulated. Some streams located in watersheds affected by wildfire and subsequent forest-regeneration efforts are home to sensitive species, including federally listed endangered or threatened salmonids. Beginning in 2025, the USGS, in cooperation with the Central Valley Regional Water Quality Control Board and the University of California Davis, will begin a research study focused on understanding the occurrence of post-fire herbicides in mountain streams downstream from recently burned commercial timberland.

Authors

• James Orlando*, U.S. Geological Survey, jorlando@usgs.gov
• Matthew DeParsia, U.S. Geological Survey
• Ashley Hernandez, Central Valley Regional Water Quality Control Board
• Annie Hall, Central Valley Regional Water Quality Control Board

*Presenting author

Poster image not available. Contact poster author directly.

Abstract

Long-term, reliable, and intercomparable datasets of environmental observations are valuable tools for informing management decisions and keeping the public informed about ecosystem health. Multiple stakeholders have an interest in the management of the California San Francisco Bay and Sacramento-San Joaquin Delta (Bay-Delta) to achieve objectives related to water quality, water supply, recreation, and ecosystem status. The U.S. Geological Survey (USGS) Biogeochemistry group, in cooperation with the Bureau of Reclamation, Sacramento Area Sewer District, San Francisco Estuary Institute, and others, has established a network of about 20 water quality monitoring stations throughout the Bay-Delta. These stations collect data at 15-minute intervals, providing real-time high-frequency measurements of water quality parameters, including temperature, specific conductivity, turbidity, dissolved oxygen, pH, dissolved organic matter (DOM) fluorescence, chlorophyll fluorescence, and nitrate concentrations. At each monitoring station, supplementary discrete water quality samples are collected approximately monthly and analyzed for nutrient and cyanotoxin concentrations, as well as identification and enumeration of phytoplankton. USGS data have been used to identify trends, understand environmental drivers, compute fluxes, and validate coupled hydrodynamic-biogeochemical models. USGS water quality monitoring stations have long periods of record with high temporal resolution, and we hope to increase awareness of the data and its potential uses in service of improving Bay-Delta science and management.

Authors

• Maura Uebner*^†, U.S. Geological Survey, muebner@usgs.gov
• Kyle Nakatsuka, U.S. Geological Survey
• Dylan Burau, U.S. Geological Survey
• Crystal Sturgeon, U.S. Geological Survey
• Tommy (Hieu) Ly, U.S. Geological Survey
• Nathan Jumps, U.S. Geological Survey
• Patrick Dellwo, U.S. Geological Survey
• Tim Baxter, U.S. Geological Survey
• Ariana Maestas, U.S. Geological Survey
• Amelia Ayers, U.S. Geological Survey
• Malanyon Adams, U.S. Geological Survey
• Tyler Beddingfield, U.S. Geological Survey
• Lane Bratz, U.S. Geological Survey
• Noelle Teske, U.S. Geological Survey
• Morgan Illman, U.S. Geological Survey
• Tamara Kraus, U.S. Geological Survey
• Brian Bergamaschi, U.S. Geological Survey
• Keith Bouma-Gregson, U.S. Geological Survey

*Presenting author, ^†Early Career Award candidate

Abstract

The Department of Water Resources (DWR) conducts continuous (15-minute interval) water quality monitoring in Suisun Marsh and Grizzly Bay, critical habitats for the endangered Delta Smelt, other native fish species, migratory waterfowl along the Pacific Flyway, and various endangered plants and animals. As part of the 2020 Incidental Take Permit (ITP) for the State Water Project (SWP), enhanced monitoring in Grizzly Bay was required to "improve measurement of temperature, salinity, turbidity, and other relevant abiotic factors." This led to the addition of three new water quality stations near the existing Grizzly Bay station, originally mandated by Water Rights Decision 1641. Two of these stations were installed as temporary buoy stations to inform management decisions regarding the Suisun Marsh Salinity Control Gate (SMSCG) Action Plan and ensure sufficient spatial coverage to detect SMSCG effects. This study evaluates the effectiveness and potential redundancy of two of these newly added stations.

We assessed whether high-frequency monitoring at these stations enhances the detection of spatial variability in water quality, or alternatively, if stations are statistically indistinguishable from their nearest counterparts. Our analysis compares data from paired regional sites before, during, and after SMSCG operations to assess redundancies in station locations and identify trends in water quality from 2018 to 2024. The four monitored stations—Montezuma Slough at Hunter Cut, Montezuma Slough Mouth at Grizzly Bay, Grizzly Bay West, and Grizzly Bay East—are managed by the Continuous Environmental Monitoring Program and the Water Quality Assessment Unit.

We compared specific conductance at these paired stations, beginning each year one month prior to gate operations and ending one month after gate operations concluded using a comparison of percent difference as a function of salinity, and a linear mixed model. We found that while the absolute percent difference between the stations can be high at lower salinities, there were no statistically significant differences between stations when looking across the entire dataset.

Authors

• Michelle Nelson^*, California Department of Water Resources, Michelle.Nelson@water.ca.gov
• Bani Badwal*^†, California Department of Water Resources, Bani.Badwal@water.ca.gov
• Vivian Klotz, California Department of Water Resources, vivian.klotz@water.ca.gov

*Presenting authors, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

The San Francisco Bay is a complex estuarine system that has been continuously monitored for water quality and suspended sediment transport since 1989. The USGS has monitored parameters such as temperature, specific conductance, turbidity, dissolved oxygen, chlorophyll, and suspended sediment concentration throughout the bay to reach a better understanding of ecological concerns and water management. Because this is such a complex tidally influenced system that has qualities of freshwater and saltwater, managing data quality can be quite a challenge. One of the biggest challenges of measuring water quality in the bay is the extreme amount of biological fouling. This fouling can include barnacles, hydroids, isopods, bryozoans, and much more. Biological fouling can grow on water quality equipment that can severely affect the accuracy and quality of the data that the USGS collects. To combat this issue, solutions like copper tape, anti-fouling paint, copper sonde guards, and frequent field visits are used. For this poster, extreme fouling and the use of anti-fouling paint are discussed to promote a better understanding of how hydrologic technicians can help increase water quality data retention and reduce biological fouling in the field.

Author

• Samantha Dittrich*^†, U.S. Geological Survey, sdittrich@usgs.gov

*Presenting author, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

The San Francisco Bay and Sacramento-San Joaquin Delta have experienced major phytoplankton- and cyanobacteria-driven harmful algal blooms (HABs and CHABs) in multiple areas in both the bay and the Delta. Satellite-based multi-spectral remote sensing imagery has been used to identify phytoplankton and cyanobacteria blooms based on chlorophyll levels in water bodies for well over a decade. This approach is highly useful for routine monitoring and to focus field sampling efforts. Recent deployments of hyperspectral airborne sensors provide the spectral resolution to support algorithms that differentiate algae and cyanobacteria by using the spectral properties of pigment reflectance. One such approach is the Spectral Mixture Analysis for Surveillance of Harmful Algal Blooms (SMASH) software package, which uses an end member mixture analysis model to identify fractional abundance of phytoplankton and cyanobacteria taxa in a waterbody. Initial results from the application of this software package to hyperspectral imagery acquired by the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS3) in September 2023 of Little Franks Tract in the Sacramento-San Joaquin Delta, and the use of a library of cyanobacterial reflectance spectra are presented here. These results confirm the potential of hyperspectral imagery to provide additional information on HAB & CHAB community composition.

Authors

• Xavier Garcia Lopez*^†, U.S. Geological Survey Bromery Intern, California Water Science Center, xgarcialopez@usgs.gov
• Brian Bergamaschi*, U.S. Geological Survey CAWSC, bbergamaschi@usgs.gov
• Dulcinea M. Avouris, U.S. Geological Survey, CAWSC
• Carl Legleiter, U.S. Geological Survey, CAWSC

*Presenting authors, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

Increased wildfire activity across the western United States has driven extensive use of fire retardants, which often contaminate nearby waterways through runoff and spray drift, impacting aquatic ecosystems. However, data are sparse, particularly for the effects of fire retardants on early life stages of Chinook salmon (Oncorhynchus tshawytscha) and Rainbow trout (Oncorhynchus mykiss). Chinook are particularly vulnerable during out-migration; and trout are a useful surrogate species that is available year-round for testing. Building on previous research on rainbow and brown trout, we are investigating both lethal and sublethal impacts of weathered and non-weathered formulations of the commonly used Phos-Chek retardant and a more environmentally-friendly formulation, Pyrocool, on two early life stages of both salmonids. Embryos and alevins were exposed to a range of concentrations over 96 hours simulating first-flush events following retardant applications. Preliminary data in Rainbow trout suggests that LC50s are in line with those previously published, and that older alevin may be more sensitive than those still retaining their yolk sacs. UV-weathered retardants were also included to represent realistic environmental conditions. Measured outcomes included mortality (LC50), hatching success, and morphological and behavioral changes. We hypothesize that the LC50 of Chinook salmon embryos and alevins will be similar to that observed in trout. We expect to observe reduced hatching success and altered behavior in individuals exposed to sublethal levels of fire retardants compared to control fish, with weathered formulations exhibiting greater toxicity than non-weathered counterparts due to increased potency following UV exposure. Overall, the goal of this study is to underscore the compounded risks posed by fire retardants in salmon habitats already stressed by climate change and pesticide residues. Results will provide critical thresholds for fire retardant concentrations in sensitive habitats, underscoring the need for fire management practices that minimize runoff into salmon-bearing waterways.

Authors

• Zoha Siddiqua*^†, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California Davis, One Shields Avenue, Davis, CA, Yolo County, 95616, USA, zsiddiqua@ucdavis.edu.
• Louise Cominassi, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA, Yolo County, 95616, USA.
• Emerson Feddor, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA, Yolo County, 95616, USA.
• Dylan Lin, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA, Yolo County, 95616, USA.
• Patrick Reece, Department of Fisheries, Wildlife and Conservation Sciences; Coastal Oregon Marine Experiment Station, Oregon State University, Newport, Oregon, 97365, USA.
• Rukmini Raman, Department of Fisheries, Wildlife and Conservation Sciences; Coastal Oregon Marine Experiment Station, Oregon State University, Newport, Oregon, 97365, USA.
• Silja Blechschmidt, Department of Fisheries, Wildlife and Conservation Sciences; Coastal Oregon Marine Experiment Station, Oregon State University, Newport, Oregon, 97365, USA.
• Susanne Brander, Department of Fisheries, Wildlife and Conservation Sciences; Coastal Oregon Marine Experiment Station, Oregon State University, Newport, Oregon, 97365, USA.
• Amelie Segarra, Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA, Yolo County, 95616, USA.

*Presenting author, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

The U.S. Fish and Wildlife Service’s (USFWS) Lodi office partnered with California Department of Water Resources (DWR) on the North Delta Food Subsidies (NDFS) Action study to measure the effects of managed flow pulses in the North Delta food web. We will use zooplankton data collected from 2019-2023 NDFS studies which encapsulates high and low water years, and controlled flow. This will be compared to catch data from the Enhanced Delta Smelt Monitoring (EDSM) program taken from areas between Lisbon Weir and Rio Vista in an effort to compare food availability and fish abundance or biomass. Zooplankton data was measured as density (individuals/m3) and fish will be assessed as total number of individuals caught or as biomass. This comparison can give insight to how various flow actions can affect food levels and fish populations in the delta.

Authors

• Lucia Arreola*^†, U.S. Fish and Wildlife Service, lucia_arreola@fws.gov
• Nicholas Veal*, U.S. Fish and Wildlife Service
• Eric Louwerens, U.S. Fish and Wildlife Service
• Paula Higginson, U.S. Fish and Wildlife Service
• Eric Holmes, California Department of Water Resources

*Presenting authors, ^†Early Career Award candidate

Abstract

The San Francisco Estuary (SFE) is a highly dynamic environment that is subject to changes both man-made and natural. Long-term monitoring is crucial to better understand the community dynamics and recruitment of fishes that use the upper estuary as a nursery. The Summer Townet Survey is one of the longest running pelagic fish sampling surveys in the state, beginning in 1959. The survey targets juvenile fish (12-55 mm FL) in the SFE to better understand fish recruitment patterns, abundance, and distribution relative to freshwater Delta outflow. More recently, this study has helped to inform actions taken to improve habitat conditions for native fish species such as Delta Smelt during the summer and fall. Summer Townet Survey provides fish, zooplankton and environmental data for the Summer-Fall Habitat Action (SFHA) and modified operation of the Suisun Marsh Salinity Control Gates (SMSCG) which are implemented under the State Water Project's Incidental Take Permit. In this study, we investigated trends in fish and zooplankton abundance and diversity during the years in which SFHA and SMSCG were implemented, and how these relate to outflow. Clarifying these patterns will provide valuable insight to assist with future management decisions.

Authors

• Margaret Johnson*^†, California Department of Fish and Wildlife, margaret.johnson@wildlife.ca.gov
• Spencer Breining-Aday, California Department of Fish and Wildlife

*Presenting author, ^†Early Career Award candidate

Abstract

The California Department of Fish and Wildlife (CDFW) has conducted long term monitoring of fish and plankton assemblages in the San Francisco Estuary (SFE) for decades. The Fall Midwater Trawl (FMWT) has sampled 100+ stations throughout the estuary September-December since 1967. The main goal of the survey is to monitor pelagic fish abundance, distribution, and recruitment patterns throughout the SFE. More recently, this study has helped to inform actions taken to improve habitat conditions for native fish species such as Delta Smelt during the summer and fall. The FMWT has conducted concurrent fish and zooplankton tows at select stations throughout the estuary since 2011. FMWT provides fish, zooplankton and environmental data for the Summer-Fall Habitat Action (SFHA) and modified operation of the Suisun Marsh Salinity Control Gates (SMSCG) which are implemented under the State Water Project's Incidental Take Permit. Long term monitoring programs like FMWT have allowed for a greater scope and comparison of food web and environmental trends in the estuary over time. This study aims to compare regional fish and zooplankton catch per unit effort (CPUE) during the years in which SFHA and SMSCG were implemented, and how these relate to outflow. Clarifying these patterns will provide valuable insight to assist with future management decisions.

Authors

• Taylor Rohlin*^†, California Department of Fish and Wildlife, taylor.rohlin@wildlife.ca.gov
• Spencer Breining-Aday*, California Department of Fish and Wildlife

*Presenting authors, ^†Early Career Award candidate

Abstract

The Yolo Bypass is critical to protecting the metropolitan and agricultural areas surrounding Sacramento, California from inundation during flood conditions. Moreover, the Yolo Bypass is the largest contiguous floodplain remaining in California’s Central Valley and constitutes critical habitat for diverse taxa of fishes including Winter- and Spring-Run Chinook Salmon and Steelhead Trout. Ecosystem-wide changes in habitat quality and connectivity have reduced instream habitat conditions and eliminated corridors for migratory fishes. Furthermore, non-native species have altered trophic interactions and habitat suitability, further complicating efforts to support native fishes in the Yolo Bypass. In effort to improve habitat conditions and increase connectivity for native fishes within the floodplain, California Department of Water Resources (DWR) is implementing a suite of landscape-scale restoration projects to promote natural floodplain processes. In collaboration with federal, state, tribal, and private entities DWR has implemented a multitude of creative projects supported by holistic monitoring and adaptive management. DWR scientists have developed and implemented several long-term projects designed to monitor fish community composition, trophic interactions, and water quality. The purpose of this presentation is to highlight multiple process-based restoration projects occurring in the Yolo Bypass floodplain, including the creation of floodplain habitat to provide enhanced food availability for juvenile salmonids and improved migratory corridors between the Yolo Bypass, Sacramento River, and northern Sacramento - San Joaquin River Delta. Projects discussed will include Yolo Bypass Salmonid Habitat Restoration and Fish Passage, Wallace Weir Fish Rescue Facility, Lower Elkhorn Basin Levee Setback, Little Egbert Slough, Lookout Slough, Prospect Island, and more.

Authors

• Brandy Smith*^†, California Department of Water Resources, brandy.smith@water.ca.gov
• Dennis Finger, California Department of Water Resources
• Hailey Mico, California Department of Water Resources
• Luke Olson, California Department of Water Resources

*Presenting author, ^†Early Career Award candidate

Abstract

The U.S. Fish and Wildlife Service (USFWS) conducts standardized electrofishing surveys throughout the Sacramento-San Joaquin Delta (Delta) to supplement Delta Juvenile Fish Monitoring Program (DJFMP) beach seine data, providing a more robust sampling of nearshore fishes. This method allows crews to sample areas that are incompatible with beach seining, particularly heavily vegetated habitats. Non-native submerged aquatic vegetation (SAV) and floating aquatic vegetation (FAV) have become more abundant in the Delta over the last two decades, leading to lower dissolved oxygen, turbidity decline, and higher water temperatures, impacting fish assemblages. Due to the rise in non-native aquatic vegetation, the California Department of Fish and Wildlife (CDFW) has funded and maintained datasets of airborne hyperspectral imagery since 2004 to map submerged and floating vegetation. Our goal is to examine the relationship between SAV, FAV, emergent marsh habitats, and fish diversity throughout the Delta for 2021 and 2022. By combining pre-existing DJFMP electrofishing data and CDFW vegetation data, we performed a multivariable analysis evaluating the impacts of different aquatic vegetation types and environmental factors on fish diversity. Increased knowledge of these relationships can help agencies make informed decisions on management of SAV and FAV throughout the Delta.

Authors

• Brian Hutchinson*^†, US Fish and Wildlife Service, brian_hutchinson@fws.gov
• Kiana Lindblad*, U.S. Fish and Wildlife Service

*Presenting authors, ^†Early Career Award candidate

Abstract

The Central Valley Project’s (CVP) Tracy Fish Collection Facility (TFCF; starting in 1957) and the California’s State Water Project (SWP) Skinner Delta Fish Protective Facility (SDFPF; starting in 1968) are fish protective facilities, which reduce fish losses associated with water exports. Fish (>20mm) are directed away from and removed from exported water (Byron, CA), and released back to the Sacramento-San Joaquin Delta, a process called salvage. The California Department of Water Resources and the United States Bureau of Reclamation are required to provide salvage information for stake holders such as the Smelt Monitoring Team and the Salmon Monitoring Team for near real time management of listed species according to their respective Biological Opinions.

The salvage database is one of the oldest databases in the state dating back to 1957 when the TFCF became operational. Initially data was stored in datasheets and in Excel files but quickly outgrew these programs. The Access salvage database became operational in 1998 and has data from 1993 to current. It currently contains more than 25 million records and is updated on a daily basis to meet real-time management needs of State and Federal Agencies. It includes the count, length and expansion metrics for calculating salvage and loss. For Salmonids, the salvage database contains tag and genetic identifications as well as associated run assignments. This poster will list data, reports, and timelines of creation in the database:

• Database structure and size
• The salvage interactive web page and FTP site for daily postings of data
• Salmon and steelhead reports for stakeholders
• Smelt reports for stakeholders
• DNA race data for salmon
• CWT tag race data for salmon
• Server location of database

Authors

• Geir Aasen*, California Department of Fish and Wildlife, geir.aasen@wildlife.ca.gov
• Tariq Celeste*^†, California Department of Fish and Wildlife
• Virginia Afentoulis, California Department of Fish and Wildlife

*Presenting authors, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

The San Francisco Estuary is a dynamic system with multiple programs studying, monitoring, and striving to understand the complexities of this large system, but there are limited opportunities for coordination and integration across these programs. BayInsights is a project supported by the EPA at the San Francisco Estuary Institute (SFEI) which endeavors to work with other programs and agencies around the San Francisco Bay to maximize sampling and monitoring efforts. The project aims to build collaboration among monitoring entities to integrate and optimize monitoring efforts, fill high-priority data gaps, and help inform management decisions or characterize ecosystem responses to specific management actions. By leveraging sampling and data across agencies, the BayInsights project is an opportunity to learn more from the data collected providing insights into nutrient trends and water quality. We will introduce the BayInsights program, outline the goals of the program, and share preliminary data from our early analyses.

Authors

• Katie Harding*, San Francisco Estuary Institute, katieh@sfei.org
• Ariella Chelsky*, San Francisco Estuary Institute

*Presenting authors

Abstract

In 2021, the California Department of Fish and Wildlife (CDFW), U.S. Bureau of Reclamation, Department of Water Resources, U.S. Fish and Wildlife Service (USFWS), National Marine Fisheries Service, and State Water Resources Control Board began a detailed technical evaluation of five long-term monitoring surveys of pelagic fishes in the San Francisco Estuary (Estuary) conducted by CDFW. The surveys reviewed were the Smelt Larval Survey, 20-mm Survey, Summer Townet Survey, and Fall Midwater Trawl. A Steering Committee was formed to provide high-level guidance on survey redesign considerations provided by a technical “Design Team” comprised of agency representatives with support by Aroon Melwani (Applied Marine Sciences, Inc) and Michael Tillotson (ICF International). The Design Team is evaluating opportunities to improve the design of existing monitoring surveys in the Estuary by exploring a standardized sample frame with various scales of volume (regions, strata, and subregions), to consistently evaluate spatial monitoring effort across surveys. Effort has included adapting and expanding upon spatial scales used by the USFWS Enhanced Delta Smelt Monitoring Study. A standardized set of CDFW spatial areas for evaluating fish species abundance and distribution has been developed throughout the Estuary. The San Francisco Bay Study (Bay Study) was recently incorporated to expand upon evaluations of spatial balance in CDFW monitoring designs to 1) assess littoral habitat relative to deeper habitat, 2) improve abundance estimates, and 3) improve spatial balance among studies. This poster will provide an update on methods and status of the CDFW sample frame refinement with inclusion of the Bay Study.

Authors

• Steven Slater*, California Department of Fish and Wildlife, Steve.Slater@wildlife.ca.gov
• Aroon R. Melwani, Applied Marine Sciences, Inc.
• Celeste Dodge, California Department of Fish and Wildlife

*Presenting author

Poster image not available. Contact poster author directly.

Abstract

The California Fish and Wildlife’s Fall Midwater Trawl spans several decades and has provided valuable information about pelagic fish population responses to environmental and anthropogenic changes. To facilitate future monitoring design improvements, a two-year special study was conducted in the fall of 2021 and 2022 to address inherent bias or uncertainty due to sampling of geographically fixed sites. Our objectives were to address two key questions: 1) what differences exist in catches between fixed site designs and stratified-random site designs?; and 2) what bias may have been introduced in understanding fish community composition, size distributions of species, and indices of relative abundance, based on catches from fixed sites only? To answer these two questions, we compared monthly samples from fixed and random sites to examine fish community composition, species diversity, regional abundance estimates with confidence intervals, and size distributions of species of concern to understand the effects of survey design on these metrics. Preliminary results suggest that fish catch and community composition was not significantly different between fixed and random stations, however variation among stations was high. This would direct attention to another focus of the survey redesign team, spatial balance inconsistencies among regions in the San Francisco Bay Delta.

Authors

• Timothy Malinich*, California Department of Fish and Wildlife, Timothy.Malinich@wildlife.ca.gov
• Steven Slater, California Department of Fish and Wildlife
• Aroon Melwani, Applied Marine Sciences, Inc.

* Presenting author

Poster image not available. Contact poster author directly.

Abstract

Automating video review processes offers several key benefits, including significant cost and time savings, as well as reduced bias and human error. However, implementing an automated computer vision pipeline requires extensive research, iterative testing, and investment in both hardware and software. FishViz, developed by Cramer Fish Science, is a computer vision project designed to automate the analysis of video data collected by the Sampling Platform. The Sampling Platform highlights how integrating rapidly advancing technologies into its scientific approach ensures innovation, accuracy, and integrity in its Bay-Delta assessments. This poster outlines the development of FishViz through three key phases:

1. Problem Identification, Research and Planning—The first step involves identifying the largest challenges of the system, including environmental factors, species-specific behaviors, and the variability of the data. Extensive research is conducted to understand these factors and select appropriate open-source object detection models. Establishing clear goals, formulating targets, and defining a timeline are critical to planning the project.
2. Model Training and Iterative Testing—Once a training dataset is built, multiple models are trained on the data. The models are then tested on videos not seen during training to identify areas of underperformance. The iterative process involves retraining and refining the models to improve accuracy and precision, until a goal is met. This can often include revisiting the research step.
3. Production, Upgrades and Optimization—As the quality of input data directly affects the model's performance, we upgraded hardware to ensure higher image quality, which in turn enhances the algorithms’ effectiveness. These improvements are an ongoing process as the field of computer vision rapidly evolves. FishViz stays on the cutting edge of both hardware and software development, as it’s continuously improved to deliver accurate, scalable, and robust results.

Authors

• Andrew Veary*^†, Cramer Fish Sciences, andrew.veary@fishsciences.net
• Kai Ross, Cramer Fish Sciences
• Bobbie Flores, Cramer Fish Sciences

*Presenting author, ^†Early Career Award candidate

Abstract

The Lodi Fish and Wildlife Office (Lodi FWO) performs fisheries monitoring sampling of the Sacramento-San Joaquin River Delta (Delta) using a standardized beach seine method to determine juvenile fish species abundance in the Delta. In recent years, boat electrofishing has been added to Lodi FWO sampling methods to supplement the data collected by beach seines and gain a better understanding of all life stages of species assemblages within the Delta, particularly in areas where beach seining is difficult. We used catch data that overlapped spatially and temporally (samples from the two surveys are within 500 m and within the same sampling week) to compare fish assemblages from 2018–2023 and identify potential limitations in each sampling method. Accordingly, we analyze differences in catches between the two methods by year, season, habitat characteristics, and environmental conditions to explain differences in catch rates between the two sampling methods. This poster represents the first step in an efficiency study that will be conducted by the Lodi FWO between beach seine and boat electrofishing sampling methods.

Authors

• Autumn Fisher*^†, U.S. Fish and Wildlife Service, autumn_fisher@fws.gov
• Jennifer Whitt*, U.S. Fish and Wildlife Service
• Jacob Stagg, U.S. Fish and Wildlife Service
• Bryan Matthias, U.S. Fish and Wildlife Service

*Presenting authors, ^†Early Career Award candidate

Abstract

Due to the steep declines of spring-run Chinook Salmon (Oncorhynchus tshawytscha) populations in the Sacramento River Basin, the Spring Run Juvenile Production Estimate (SR-JPE) program was developed to monitor the annual number of outmigrating spring-run Chinook juveniles. To achieve accurate counts, the Genetic Monitoring (GeM) Lab at the California Department of Water Resources utilizes genotyping workflows (GT-seq and CRISPR-based SHERLOCK) to distinguish spring-run from the other Central Valley Chinook Salmon runs (fall, late fall, and winter). Based on the need for rapid and precise identification of the roughly 2,000+ samples collected each year for the SR-JPE, optimizing the sample collection and processing workflows for field and lab crews is critical. The current method for tissue collection includes the direct insertion of fin clips into tubes containing a custom rapid DNA extraction buffer (2% Proteinase K, 98% Low TE). While this collection method was relatively successful for the 2024 JPE, effective preservation of the DNA relies on maintaining the temperature of the buffer pre- and post-collection at 4°C and -20°C, respectively. This introduces the potential for complications during transport and storage of the sample tubes and tissues before they are returned to the lab. For this project, we aim to explore an alternative method of fin clip preservation where a sample is placed onto Whatman paper and allowed to dry inside a collection tube (rather than in coin envelopes, which are typically used to hold dry fin clip specimens). This dry preservation technique reduces processing time by facilitating the direct addition of DNA extraction buffer in the lab and streamlines field collections by eliminating the need for buffer temperature control.

Authors:

• Emma Freedman*^†, California Department of Water Resources, Emma.Freedman@water.ca.gov
• Melinda Baerwald, California Department of Water Resources
• Sarah Brown, California Department of Water Resources
• Sean Canfield, California Department of Water Resources

*Presenting author, ^†Early Career Award candidate

Abstract

Zooplankton are a crucial part of food web dynamics that support Bay-Delta fish, including threatened or endangered species. Zooplankton monitoring collections are carried out by five CDFW surveys using three different gear types for IEP, in which 1,500 total samples are collected annually. Processing these samples is time-consuming and requires expertise. This project evaluates the use of image-based classification (“Deep Learning”) modeling to identify and count the zooplankton species in IEP survey samples. These auto-detection methods have the potential to reduce processing and reporting time, and to improve data quality.

The application of image-based deep learning is optimized with large reference image libraries (a high number of images per class). We used culturing methods to propagate zooplankton species that were collected with pump sampling (micro-zooplankton) by the Environmental Monitoring Program survey (Department of Water Resources). We imaged the zooplankton cultures using a FlowCam 8001 (Yokogawa Inc).

We used the web-based deep learning model, Ecotaxa, to test the strength of our reference library. We pre-processed images using the Zooprocess software package to segment objects from raw FlowCam images, standardize backgrounds, and generate image filter data. We uploaded images and associated data to Ecotaxa and validated species identification to establish a primary “project” (a collection of images that have been sorted against validated images by the deep learning tool) having three taxa classifications.

For testing, we exported the primary project library and set a randomized subsample to the ‘unknown’ status. These, together with the remainder as the test library, were uploaded to a test project in Ecotaxa. The resulting Ecotaxa class predictions for the unknowns were 99.3% accurate.

With this early deep-learning classification success, image library development and testing efforts will be continued in order to support accurate identification of all 23 micro-zooplankton classes documented in IEP surveys.

Authors

• Katherine Hostetler*^†, IEP, Katherine.Hostetler@wildlife.ca.gov
• Karrin Alstad^*, IEP, Karrin.Alstad@wildlife.ca.gov
• Kristi Arend, U.S. Fish and Wildlife Service
• Marie Garcia, University of California Davis, Department of Pesticide Regulation

*Presenting authors, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

Released by Esri in 2020, the United States Geological Survey (USGS) California Water Science Center Estuarine Hydrodynamics and Sediment Transport Group (EHST) has been utilizing the ArcGIS Field Map (AGFM) mobile app since 2022. AGFM allows field staff to access important geographic data sources from a mobile phone. Staff using AGFM can: find a station in relation to their current location; measure distances; locate established site information such as standard cross sections; access GIS layers within the app for additional information about a station; locate marinas and boat launches; identify river names and much more. The mobile phone app can be easily used by anyone who has no background in GIS and the EHST uses AGFM as a learning tool for new staff. In addition, the robust offline capabilities of AGFM ensure continued functionality in the field even where Wi-Fi-internet coverage may be scarce. By incorporating ArcGIS Field Map into standard field workflows, Estuarine Hydrodynamics and Sediment Transport Group staff have increased efficiency in field operations through quick access to critical station and safety information.

Author

• Lawrence Fujiwara*, U.S. Geological Survey, hfujiwara@usgs.gov

*Presenting author

Poster image not available. Contact poster author directly.

Abstract

The Aquatic Species and Habitat Sampling Platform (Sampling Platform) is a novel sampling system that assesses fish communities across various habitat types using low impact sampling. We have successfully deployed the Sampling Platform in the Bay-Delta, where the presence of sensitive or protected species requires a less invasive sampling approach. The Sampling Platform passively samples fish using a pass-through video camera system to elucidate habitat associations while minimizing stress and mortality compared to traditional sampling methods. The videos captured by the Sampling platform have primarily been reviewed by humans, which can be time consuming and costly. Machine learning and computer vision offer an opportunity to reduce processing time and expenses. We aim to optimize the video review process by integrating a machine learning model known as FishViz, which can automatically detect and enumerate fish. We identified videos containing few fish as an early point of integration, as this would reduce time spent manually reviewing footage of an empty live box, while minimizing the risk of greatly undercounting fish. We performed analyses comparing FishViz to human reviewers, focusing on the frequency and magnitude of over and undercounting fish. These analyses showed that the current FishViz model could be reliably integrated into the review process for videos in which it detected 10 fish or fewer. For such videos, human reviewers can verify observations produced by FishViz, thus eliminating the need to watch the entire video. This combination of manual and automated review has improved the overall video review process. It can be further improved and expanded as better FishViz models are developed, and more sophisticated recording equipment is employed on the Sampling Platform. Such advances will allow for increased volume and reduced processing time for high-quality fish community data in the Bay-Delta.

Authors

• Mitch Gladding*^†, Cramer Fish Sciences, mitch.gladding@fishsciences.net
• Kai Ross, Cramer Fish Sciences
• Andrew Veary, Cramer Fish Sciences
• Jesse Wiesenfeld, Cramer Fish Sciences

*Presenting author, ^†Early Career Award candidate

Abstract

There are four seasonal runs of Chinook Salmon that migrate through the Delta and Central Valley. Over the years, there has been a trend of declining populations of winter and spring-run salmon, which has led to their respective listings as endangered and threatened, while fall and late fall-runs remain unlisted. Accurate Chinook Salmon run identification is critical to inform water management decisions but is challenging due to temporal and spatial overlap of runs and an inability to distinguish them visually. In the Genetic Monitoring (GeM) lab at the Department of Water Resources, we utilize cutting-edge genetic monitoring methods like the CRISPR-Cas13a SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) assay, to obtain accurate run assignments for individual Chinook Salmon. Rapid and accurate genetic run identification is essential for mandated work such as Spring-run JPE (Juvenile Production Estimate) and Salvage operations. Our laboratory currently uses an Agilent Biotek Synergy H1 fluorescence reader for all SHERLOCK reactions. However, to build capacity and redundancy, we have optimized a protocol to use another machine (QuantStudio qPCR system) to support SHERLOCK-based assays. Adding redundancy in our laboratory gives us the ability to continue processing samples while either machine is down for maintenance (or use on other projects, etc.) Here, we will present the steps we took to ensure that this sensitive procedure can be performed using multiple platforms.

Authors:

• Pachia Lee*^†, California Department of Water Resources, pachia.lee@water.ca.gov
• Scott Meyer, California Department of Water Resources
• Emma Freedman, California Department of Water Resources
• Sean Canfield, California Department of Water Resources
• Sarah Brown, California Department of Water Resources
• Melinda Baerwald, California Department of Water Resources

*Presenting author, ^†Early Career Award candidate

Abstract

The Georgiana Slough Salmonid Migratory Barrier (GSSMB) is designed to be a “non-physical” barrier to reduce the entrainment rate of out-migrating juvenile salmonids into Georgiana Slough where their survival rate is much lower. The barrier consists of subsurface frames with sound projectors, flashing lights, and orifice lines that create a bubble curtain. This combination of deterrents is intended to discourage salmonids from traveling into Georgiana Slough.

Traditional boat-mounted Acoustic Doppler Current Profiler (ADCP) mapping was performed across a range of flow conditions, but spatial resolution is limited to single transect locations. In addition, air (produced by the GSSMB) severely hinders the efficacy of acoustic-based equipment to measure velocity. To better understand velocity patterns and the influence of the bubble curtain on the flow field, we employed a small Uncrewed Aircraft System (sUAS) outfitted with the River Observing System (RiOS) payload developed in collaboration with the National Aeronautics and Space Administration (NASA).

The combination of boat-based and aerial mapping provides distinct, yet complementary measurements of velocity and bubble fields near the GSSMB. Observations were made over a range of varying flow conditions and GSSMB configurations (bubbles on and off) and these data will yield novel insight into both the near-barrier and reach-scale velocity fields.
(Results will be provided by way of maps and figures of the region).

Authors

• Trevor Violette*, U.S. Geological Survey, California Water Science Center, tviolette@usgs.gov
• Dr. Carl Legleiter, U.S. Geological Survey, Observing Systems Division
• Paul Kinzel, U.S. Geological Survey, Observing Systems Division

*Presenting author

Abstract

Biomonitoring programs often target taxa that differ in generation times. However, sampling frequencies that may be adequate for longer-lived organisms may be too coarse to detect fine-scale dynamics in fast-fluctuating taxa. Different statistical techniques are available to interpolate abundances between sampling periods, and thus ‘upsample’ coarse biomonitoring data to facilitate comparison between populations. However, limited research has examined the precision and ability of these techniques to capture populations’ peaks and troughs. Here, we sought to assess the efficacy of two interpolation methods (LOESS smoothing and cubic splines) on data from the monthly IEP Zooplankton Monitoring Program. Using data spanning 1972-2021 from sampling station NZ064 in the Delta, we upsampled biomonitoring data collected at monthly time-steps into a consistent daily frequency. We focused on the abundance of Bosmina spp., a cladoceran common throughout the San Francisco Bay Estuary. While both methods produced daily time series, LOESS generally had higher mean square error (MSE 1.93) than cubic splines (MSE 0.884), indicating that LOESS predictions generally diverged more from observed data relative to cubic splines. In addition, tests evaluating distributions of predicted vs. observed data revealed that some facets of these divergences may not necessarily be captured by MSE alone, and thus may be worth exploring in detail. We also explored how recent advances in complex network structures (e.g., Recurrent Neural Networks) can improve efforts by integrating environmental covariates and multiple streams of data (e.g., across nearby stations), effectively transferring statistical power from data-rich to data-poor moments and places. We show that advances in time-series methods can enable a wide range of ecological applications that require evenly-spaced, high-frequency data. However, these exercises should be carefully validated via specific tests designed to challenge whether upsampled data aligns with expected ecological dynamics.

Authors

• Tyler Marino*^†, Department of Environmental Science, Policy, and Management, University of California, Berkeley, tcmarino8@berkeley.edu
• Robert J. Fournier, Department of Environmental Science, Policy, and Management, University of California, Berkeley
• Stephanie M. Carlson, Department of Environmental Science, Policy, and Management, University of California, Berkeley
• Albert Ruhi, Department of Environmental Science, Policy, and Management, University of California, Berkeley

*Presenting author, ^†Early Career Award candidate

Abstract

In October 2024, the California Department of Fish and Wildlife’s Office of Training and Development published a new interactive training program, “Identification of Common and Protected Fish Species at the Skinner Delta Fish Protective Facility,” that generated immediate interest from other fish identification trainers. Interactive presentations are an attractive alternative to in-person training because they are repeatable as needed, easy to schedule around other duties, and allow for interactive features that can deepen learning, but the perception that they can be time consuming and complex to develop may put off trainers contemplating one. The CDFW Fish Facilities and Larval Entrainment Unit delivers fish identification training to staff at the Skinner Delta Fish Protective Facility, covering dozens of species from diverse fish families, including protected species. To realize the benefits of interactive trainings described above, staff from the Fish Facilities and Larval Entrainment Unit collaborated with staff from the Office of Training and Development to create an interactive fish identification training. Using the existing fish identification presentation as a template, we generated a script for a training development software. Further, our efforts led to organized visits, in coordination with staff from CDFW’s Office of Communications, Education and Outreach and the Federal Bureau of Reclamation, to obtain high quality images of fish specimens. The final product provides voice overs to the slides and interactive quizzes to verify learning. An open flow of communication and regular meetings allowed the subject matter experts to fine-tune biological details and test the pacing of the material, while the training and development specialist contributed options for attractive formatting and effective message delivery. This collaborative format allowed each of the participants to contribute their strongest skills to the polished final project. Interested trainers can use this poster as guide to “stop worrying” and develop their own projects.

Authors

• Walter Griffiths*, California Department of Fish and Wildlife, Walter.Griffiths@wildlife.ca.gov
• Virginia Afentoulis, California Department of Fish and Wildlife
• Tariq Celeste, California Department of Fish and Wildlife
• Marco Valencia, California Department of Fish and Wildlife

*Presenting author

Abstract

Green and White Sturgeon are two closely related anadromous fish species that migrate throughout the San Francisco Estuary (SFE), including the Delta, and surrounding Napa, Sacramento and San Joaquin River watersheds. Sturgeon are a long-lived, late-spawning species with highly variable life histories across individuals, adapted to the variable environmental conditions in California’s Central Valley and the Pacific Ocean. Both species are impacted by water diversions, habitat modifications, over-fishing, and water contaminants from agricultural, mining and industrial activities. During the summer of 2022, an unprecedented harmful algal bloom (HAB) caused widespread toxins in the SFE, leading to extensive fish mortality, including sturgeon.

This study utilizes geochemical analysis of pectoral fin rays to reconstruct the age and migratory histories of sturgeon collected during and outside of the HAB event. By comparing age structures and migratory patterns, we aim to identify specific migratory phenotypes which may have been disproportionately affected by the HAB. Preliminary findings suggest a potential for habitat-specific vulnerabilities tied to migratory behavior. This research provides critical insights into how environmental stressors impact sturgeon populations, informing adaptive management strategies for these threatened and economically significant species.

Authors

• Jamie K. Sweeney*, Cramer Fish Sciences, jamie.sweeney@fishsciences.net
• James Hobbs, Otolith Geochemistry and Fish Ecology Laboratory, University of California Davis
• Kirsten Sellheim, Cramer Fish Sciences
• Malte Willmes, Norwegian Institute for Nature Research
• Levi Lewis, Otolith Geochemistry and Fish Ecology Laboratory, University of California Davis

*Presenting author

Abstract

The monitoring network in the San Francisco Bay-Delta consists of a variety of sampling methods. As a result, it can be challenging to compare fish community results across sampling gears and study designs. The U.S. Fish and Wildlife Service’s (USFWS) Lodi office, conducts electrofishing as part of the Delta Juvenile Monitoring Program (DJFMP) to measure the biodiversity of nearshore habitat for fishes of the Sacramento – San Joaquin Delta. In response to managers’ requests to better understand fish assemblage trends in the San Francisco Bay-Delta, we will summarize fish count and biomass data across Delta regions and seasons. Our goal is to present preliminary community visualization tools and metrics that can also be used to explain trends using data from other gears like beach seines and trawls.

We will use DJFMP electrofishing data collected from 2021-2023 which encompasses six major regions that span latitudinally from the Sacramento River’s connection with Steamboat Slough down to Mossdale Crossing Regional Park on the San Joaquin River and longitudinally from the Mokelumne River across to the confluence near Sherman Island. Fish catch will be assessed as biomass per second shocked compared to individuals caught per second shocked. Biomass was calculated based on length weight relationships using average condition factors. We used biomass as an estimate to assess community makeup to account for different body shapes and growth rates. Using this data we hope to address, seasonal migration of fishes and assess regional productivity through these six major regions across flood and drought years.

Authors

• Nicholas Veal*^†, U.S. Fish and Wildlife Service, nicholas_veal@fws.gov
• Jacob Stagg, U.S. Fish and Wildlife Service
• Adam Nanninga, U.S. Fish and Wildlife Service
• Eric Huber, U.S. Fish and Wildlife Service

*Presenting author, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

Sacramento pikeminnow (Ptychocheilus grandis/SAPM) are a temperature resilient native fish that reside in the Sacramento-San Joaquin River Delta (Delta). The Delta experiences large variability in its water temperature. Within 100 years, it is predicted that the Delta will have an overall increase in water temperature. SAPM migrate up North of the Delta in order to reach spawning grounds. This movement up North can be triggered earlier by warmer water temperatures, possibly creating a shift in seasonal numbers. As climate change predictions show an increase in water temperature, we could see a shift in SAPM catch numbers throughout different regions of the Delta. Currently, there is no recent analysis on the effects of water temperature on the population density of SAPM. This study aims to determine if there is a correlation between water temperature and catch number of SAPM within the Delta. Lodi Fish and Wildlife’s Delta Juvenile Monitoring Program’s Seine data gathered from 1976-2023 contains water temperature and SAPM catch numbers. The data will be analyzed through R and fit to a linear regression model depicting the number of catches of SAPM versus seasonal water temperature throughout the years. A map of the Delta will also be created to display the water temperature and catch number of SAPM in different regions for 1976 vs 2023. Based on the results of this model we can predict if there will be a change in SAPM catch numbers with increasing temperatures. This will provide needed information that may have an impact on their future conservation.

Authors

• Pamella Asnata*, U.S. Fish and Wildlife Service, pamella_asnata@fws.gov
• Jordan Besson*, U.S. Fish and Wildlife Service

*Presenting authors

Abstract

Splittail (Pogonichthys macrolepidotus) are endemic cyprinids of the San Francisco Estuary that depend on flooded seasonal wetlands for successful spawning. Splittail populations are equipped to survive drought years because individuals are long-lived with high fecundity that allow populations to rebound. However, habitat loss, contaminants, and extended drought periods still threaten Splittail survival. Splittail were listed as a threatened species by the United States Fish and Wildlife Service (USFWS) between 1999-2003 and remain a Species of Special Concern in California. Understanding the long-term abundance and recruitment of these native fish is challenging because of their inherent recruitment variability tied to the increasingly variable Mediterranean climate and floodplain inundation in California’s Central Valley. We analyzed 25 years (1999-2023) of beach seine data collected by the USFWS Delta Juvenile Fish Monitoring Program to examine trends in age-0 Splittail catch. We hypothesized that catch per unit effort (CPUE) of age-0 Splittail would be significantly higher in wet years than dry years, but that overall CPUE has declined since 1999. After comparing a set of candidate models and accounting for variability in annual Delta discharge, Splittail abundance appeared to have increased. Our results also supported previous work demonstrating that Splittail abundance and recruitment was higher in wet years than dry years. Next, we analyzed Splittail catch, over the same time period, from the Yolo Bypass Fish Monitoring Program and salvage data from the Tracy Fish Collection Facility and the Skinner Delta Fish Protective Facility. The pattern of higher age-0 abundance in wet years was seen across all datasets, but patterns after correcting for Delta discharge were variable. Our results convey a variable Splittail population over 25 years, but also possibly increasing Splittail spawning or recruitment success in wet years, suggesting that current conservation and restoration efforts may have a positive effect on this species.

Authors

• Savannah Valdez*^†, U.S. Fish and Wildlife Service, savannah_valdez@fws.gov
• Vivian Peck*, U.S. Fish and Wildlife Service
• Geoffrey Steinhart, U.S. Fish and Wildlife Service

*Presenting authors, ^†Early Career Award candidate

Abstract

In a rapidly changing environment, innovative tools like population genomics can provide valuable knowledge for more informed decision making in invasive species management. Three species of true loaches (Cobitidae) have been identified in California’s Central Valley; Large-Scale Loach Paramisgurnus dabryanus, Fine-Scale Loach Misgurnus mizolepis and Pond Loach Misgurnus anguillicaudatus. Our study consisted of three phases. In phase one, we developed a qPCR assay to detect the eDNA from loaches then deployed a paired sampling design to compare detections of eDNA and minnow traps in canals and ponds at the San Luis National Wildlife Refuge (SLNWR). In spring 2023, we conducted phase two where we trapped and removed hundreds of invasive Cobitids from the SLNWR guided by eDNA detections. The main goal of phase three was to utilize genomic population analyses to provide regional Aquatic Invasive Species (AIS) managers knowledge of the loach population size and genetic resiliency. Tissue samples (fin clips) from 656 loaches captured in phase two were genotyped using the microsatellite loci to create multi-locus genotypes for each tissue analyzed. Various scenarios were possible: (1) Low diversity- if the population was started by a few individuals, the population may have decreased environmental and reproductive fitness. This scenario would lead to a bottleneck for the population which could be strengthened through continued removal efforts. (2) Intermediate diversity- the effective population size could be determined as well as the impact of the removal effort on the population size. This could inform future management decisions and allocation of resources. (3) High diversity- the source of invasion could be identified, informing prevention efforts to lower risks of any further introduction or additions to the population. Together, the three phased study aims to create a new framework for developing actionable information about newly discovered invasive species.

Authors

• Jennie J. Wiggins*^†, U.S. Fish and Wildlife Service, jennie_wiggins@fws.gov
• Scott Blankenship, Genidaqs - A Cramer Fish Sciences Laboratory
• Vanessa Tobias, U.S. Fish and Wildlife Service

*Presenting author, ^†Early Career Award candidate

Abstract

The Yolo Bypass is the largest floodplain in the Sacramento River- San Joaquin Delta and provides critical habitat for native fishes. As a component of the Yolo Bypass Fish Monitoring Program (YBFMP), secchi depth measurements (m) , turbidity (FNU), chlorophyll (ug/L), and light attenuation (μmol s– 1m– 2) data are collected from one station in the Yolo Bypass (Screw Trap at Toe Drain, STTD) and one station in the Sacramento River (Sherwood Harbor, SHR) every two weeks throughout the year. As a part of a scientific review conducted by YBFMP, we explored the methods, use and efficacy of the light attenuation data. Using this data, we calculated KdPAR which is the diffuse attenuation coefficient of photosynthetically active radiation and is commonly used to predict light attenuation in aquatic productivity models. We expect to find higher kdPAR values in the Sacramento River when compared to the Yolo Bypass which will result in a larger photic zone and higher primary productivity. To evaluate the data collected by YBFMP and test our hypothesis, we used kdPAR to predict the depth of the photic zone used chlorophyll as a proxy for phytoplankton abundance. Analyzing multiple years allowed us to compare seasonal change and differences in the depth of photic zone between water year types. Predicting the depth of the photic zone can be great representation of the productivity of the Yolo Bypass and Sacramento River and provide important insight into the ecological health of these systems.

Authors

• Alexa Camilleri Evans*^†, California Department of Water Resources, alexa.camillerievans@water.ca.gov
• Luke Olson*, California Department of Water Resources

*Presenting authors, ^†Early Career Award candidate

Abstract

As part of a multi-investigator study of harmful algal blooms (HABs) along the San Francisco Estuary salinity gradient, we conducted sampling at four shore stations in Suisun Bay and Carquinez Strait for microcystin and domoic acid (DA) algal toxins. Several approaches were employed including discrete water sampling, Solid Phase Adsorption Toxin Tracking (SPATT) passive samplers, and analysis of invertebrate tissues. Stations were sampled every two weeks from April to September and approximately monthly for the rest of the year. Here we report results from one station located in the estuary mesohaline region at the western end of the Carquinez Strait. Water samples were collected using a Van Dorn bottle and filtered for analysis. SPATT samplers were deployed during each sampling event for 48h and approximately one month. Baited minnow traps were deployed onto the sediment surface for 48 h and all invertebrates were identified, measured and frozen for analysis. Toxin analysis was performed by liquid chromatography - mass spectrometry. DA, associated with the marine diatom-HAB Pseudo-nitzschia was regularly observed in both SPATT and tissue samples, but rarely seen in grab samples. Microcystin congeners, indicative of freshwater cyanoHABs such as Microcystis, were less frequently observed in SPATT compared to DA, and were recorded seasonally, being present in summer and autumn but absent in winter and spring samples. Microcystin was detected in the majority of tissue samples. These results confirm that algal toxins, representative of marine and freshwater HABs, are regularly present in the mesohaline portion of the San Francisco Estuary and suggests that transport of toxins from both upstream and seaward habitats may be important in explaining their presence there. Additionally, sampling for HAB toxins only by analyzing discrete water samples may underestimate toxin presence and provide an incomplete picture of the role of HABs across the estuary.

Authors

• Alexandra Johannsen*^†, California State University Maritime Academy, ajohannsen58@csum.edu
• Alex E. Parker, California State University Maritime Academy
• Ellen Preece - California Department of Water Resources
• Keith Bouma-Gregson, U.S. Geological Survey
• Crystal Sturgeon, U.S. Geological Survey
• Amelia Ayers, U.S. Geological Survey
• Raphael Kudela, University of California Santa Cruz

*Presenting author, ^†Early Career Award candidate

Abstract

Fish populations in the San Francisco Estuary (SFE) have been declining for decades due to multiple interacting factors, including a reduction in tidal wetlands and a decline in zooplankton abundance throughout the estuary. Tidal wetlands in the SFE are being restored to enhance fish populations by providing beneficial habitat and food web resources, such as a richer zooplankton assemblage than in open waters. Longfin smelt (LFS; Spirinchus thaleichthys) is a declining native fish and a threatened species. Copepod abundance in wetlands directly affects LFS populations, since larval LFS rely on copepods as their primary food source. The purpose of this in progress study is to identify food web resources in close proximity to wetland restoration sites, compare them with ecological indicators in wetlands at different stages of restoration (early, intermediate, mature), and identify zooplankton indicator species associated with beneficial habitat for LFS. High-throughput sequencing (HTS) will be utilized to identify the diversity of prey available in the water column, including calanoid and cyclopoid copepods (Eurytemora carolleeae, Acanthocyclops americanus, Acanthocyclops robustus, Pseudodiaptomus forbesi), and indicator species in diets of larval fishes, specifically LFS, Pacific herring (Clupea pallasii), and Prickly sculpin (Cottus asper), which use wetlands as nursery grounds during the same time of year as LFS. HTS is advantageous for DNA diet analysis as it can identify diverse zooplankton in the diets of larval fishes, including species not previously described as a food source that microscopy was not able to identify. HTS will identify the DNA of prey consumed by the larval fishes, ambient zooplankton species available to the larval fishes, and indicator species at each wetland restoration site. This study will expand upon current limited databases for copepod identification, provide information for zooplankton monitoring near wetlands, provide information for wetland restoration managers; including prey availability of species of zooplankton for larval fishes in their nursery grounds, an understanding of how these prey differ across wetlands at different stages of restoration, and key characteristics of wetlands that support zooplankton abundance and larval fish populations, which will ultimately benefit declining fish populations in the SFE.

Authors

• Anthony Donahue*^†, San Francisco State University, Estuary and Ocean Science Center, adonahue1@sfsu.edu
• Erick Ortiz, San Francisco State Univ., Estuary and Ocean Science Center
• Anne Slaughter, San Francisco State Univ., Estuary and Ocean Science Center
• Wim Kimmerer, San Francisco State Univ., Estuary and Ocean Science Center
• Michelle J. Jungbluth, San Francisco State Univ., Estuary and Ocean Science Center

*Presenting author, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

Estuarine turbidity maxima (ETMs) are localized areas in estuaries that concentrate zooplankton, phytoplankton, detritus, and suspended sediment which can provide crucial habitat for native fishes such as delta smelt in the low salinity zone of the San Francisco Bay Estuary. ETMs are characterized by high suspended sediment concentrations and turbidity due to the interactions between denser, high salinity oceanic water and low salinity river flow. In the San Francisco Bay Estuary, ETMs are hypothesized to form when the 2 ppt isohaline (X2) is positioned in deep channels during periods of tidal asymmetry. In other estuaries, ETMs are some of the most productive regions due to the high concentration of lower trophic food web resources.

The Directed Outflow Project ETM Study was developed to see if food resources for planktivorous pelagic fish were concentrated in ETMs. We hypothesize that the presence of ETMs will predict higher abundances of zooplankton. Macrozooplankton and mesozooplankton tows were conducted at the surface and bottom of the water column from Suisun Bay up to the lower Sacramento River from June through November. Sites were categorized as inside the ETM or outside of the ETM based on stratification of salinity and turbidity at each site in when tidal parameters predicted development of an ETM. We plan on running generalized linear models to examine the influence of multiple variables including predicted presence of an ETM, turbidity, and salinity on zooplankton abundance.

Authors

• Calvin Akiyama-Lee*, ICF, Calvin.AkiyamaLee@icf.com
• John Brandon, ICF
• Teague Corning, ICF
• Andrew Kalmbach, ICF

*Presenting author

Poster image not available. Contact poster author directly.

Abstract

This project is part of an ongoing effort to assess the transport of the copepod Pseudodiaptomus forbesi between the Cache Slough Complex (CSC) and surrounding habitats in the northern Delta. Pseudodiaptomus forbesi is an abundant introduced copepod that is an important food source for small fish. While net fluxes of zooplankton such as P. forbesi out of wetlands have been suggested as justification for restoration, there is little evidence that such fluxes occur. The day/night vertical migration behavior of P. forbesi may play a role in the net transport of this species: adult copepods are abundant in shallow water only at night and remain on the bottom during daylight. A 2018 field study in Wildlands marsh in the northern CSC found that this pattern of vertical migration interacted with a summertime asymmetry in tidal currents (stronger daytime ebbs and stronger nighttime floods) to produce a long-term net flux into the wetland. This project is an effort to determine if this pattern is consistent across the CSC. To do so, we utilized data on P. forbesi abundance from multiple field studies to develop an algorithm that predicts proportions of copepods in the water column based on turbidity and water depth. This algorithm will then be applied to long-term flow and turbidity data from six sites in the CSC to calculate net copepod fluxes over similar time periods to the 2018 study. These calculated fluxes will quantify the interaction between the vertical distribution of P. forbesi (modulated by turbidity and water depth) and tidal currents to determine if the long-term horizontal movement patterns of this copepod at locations across the CSC are consistent with the 2018 study’s findings. The results of this project will provide a basis for subsequent hydrodynamic modeling to characterize these movement patterns in greater resolution throughout the CSC.

Authors

• Charles Norton*^†, Estuary and Ocean Science Center, San Francisco State University, cnorton1@mail.sfsu.edu
• Wim Kimmerer, Estuary and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA 94920
• Anne Slaughter, Estuary and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA 94920
• Toni Ignoffo, Estuary and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA 94920

*Presenting author, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

Estuarine turbidity maxima (ETM) may play a crucial role in primary and secondary productivity in the San Francisco Bay and Delta by concentrating suspended sediment, detrital matter, and organisms in brackish areas. The hydrodynamics of these zones are complex due to the horizontal salinity gradient, which creates a two-layer flow exchange (gravitational circulation) near the 2-PSU isohaline and are predicted in-part by tidal cycles. The gravitational circulation causes increased turbidity, detritus, and vertical mixing of phytoplankton taxa. Understanding the effects of this physio-chemical process on primary productivity is crucial to predicting where food resources may be accumulating.

The U.S. Bureau of Reclamation’s Directed Outflow Project was established in part to identify the drivers of primary and secondary production to benefit Delta smelt. In the late spring to fall of 2024, ICF surveyed predicted ETMs and collected data on water quality parameters, zooplankton, and phytoplankton. As part of this study, we seek to clarify (1) how chlorophyll varies within the water column (i.e., comparison between surface and bottom samples) of predicted ETMs spatiotemporally and (2) how chlorophyll degradation (i.e., comparisons between chlorophyll-a to phaeophytin ratios) compares within and outside a predicted ETM. Chlorophyll-a can be used as a proxy for biomass, while phaeophytin can be used as proxy for algal health. Lower concentrations of chlorophyll-a to phaeophytin may indicate high algal stress/turnover. We anticipate higher concentrations of chlorophyll-a near the surface due to light penetration and algal photosynthetic needs. As turbidity, nutrients, and organisms are attenuated and shuffled in ETMs, we anticipate higher concentrations of chlorophyll-a and chlorophyll-a to phaeophytin ratios in ETMs compared to non-ETMs, indicating the presence of high productivity within these zones.

Authors

• Crystal Garcia*^†, ICF International, crystal.garcia@icf.com
• Caitlin Hall*, ICF International
• Andrew Kalmbach, ICF International
• Calvin Y. Akiyama-Lee, ICF International

*Presenting authors, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

There is no time-series of measured phytoplankton primary productivity in the San Francisco Estuary Delta (SFED) to evaluate levels during the start of the Pelagic Organism Decline (POD). Here, using statistically described relationships between nutrients and primary productivity, the EMP 43-year historical time-series of nutrients is interrogated and used to estimate primary production from 1979 to 2022.

Authors

• Richard Dugdale*, Estuary and Ocean Science Center, San Francisco State University, rdugdale@sfsu.edu
• Alex Parker, California State University Maritime Academy
• Frances Wilkerson, Estuary and Ocean Science Center, San Francisco State University

*Presenting author

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Abstract

Dead-end channels in the Sacramento-San Joaquin Delta are known to frequently support cyanobacteria harmful algal blooms (cyanoHABs), which can exceed water quality standards. Cyanobacteria possess gas vacuoles that enable them to float to the surface, in some cases forming dense blooms and outcompeting beneficial phytoplankton species, which can sink below the photic zone without sufficient mixing energy. The low-energy dynamics of dead-end channels may promote cyanoHAB formation in certain conditions but remain understudied in the Delta. To study the hydrodynamics of dead-end channels, we conducted a field study in the Stockton waterfront during August 2024, instrumenting three sites chosen to span a variety of wind and tidal forcing as the channel shallows and curves into a dead end. We instrumented each site with a vertical array of temperature sensors and water quality sondes, and deployed anemometers and upward-facing acoustic doppler current profilers (ADCPs) at two sites to capture wind velocities and net-flow throughout the water column. We use an energy balance approach to investigate the stability of the water column and compare the sites in Stockton’s dead-end channel to hydrodynamic observations in Delta main channels. We observed frequent diurnal stratification in the top 1–2 m of the water column with mixing occurring overnight. Stratification was strongest in the channel’s dead-end where afternoon temperature differences between the surface and mixed layer reached 3–4 °C. During a strong wind event (velocities >6 m/s), stratification did not occur, and a recovery period of several days occurred before stratification resumed at its previous extent, providing insight into the effects of mixing and relative contributions of wind and tidal forcing. Ongoing analyses will characterize the vertical distribution of phytoplankton and water quality indicators to assess how hydrodynamics affect phytoplankton biomass and community composition. These findings will support the identification of hydrodynamic processes, gradients, and thresholds underpinning the formation of cyanoHABs in low-energy regions of the Delta.

Authors

• Tia Böttger*^†, U.S. Geological Survey, tbottger@contractor.usgs.gov
• Sienna White, University of California Berkeley
• Mark Stacey, University of California Berkeley
• Evan Variano, University of California Berkeley
• Brian Bergamaschi, U.S. Geological Survey
• Lisa Lucas, U.S. Geological Survey
• Keith Bouma-Gregson, U.S. Geological Survey

*Presenting author, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

The Sacramento-San Joaquin Delta is experiencing a growing diversity of cyanobacterial harmful algal blooms (cyanoHABs), with significant implications for water quality, ecosystem health, and public safety. Over the course of eight months in 2023, we conducted a comprehensive study across 10 sites, combining whole-genome metagenomics, cyanotoxin profiling, and detailed water quality assessments. Sampling efforts were expanded into the north and south Delta during July and October 2023 to better capture spatial dynamics and identify the environmental drivers influencing their diversity and dominance.
In our samples, we were able to assemble more than 50 genomes from multiple cyanobacterial genera, including Microcystis, Aphanizomenon, Dolichospermum, Planktothrix, and Cyanobium. Our findings revealed distinct seasonal shifts in community structure, with different cyanobacterial taxa dominating in spring, summer, and fall. Key factors, including nitrogen availability and hydrological conditions, shaped the co-occurrence and spatial distribution of nitrogen-fixing and non-nitrogen-fixing cyanobacteria, as well as the dominance of specific species. Additional analyses will further characterize the environmental variables associated with different cyanobacterial species and strains in the Delta. These results emphasize the importance of spatially resolved sampling to understand the occurrence of different species and strains.
This study highlights the complexity of environmental conditions driving cyanobacterial diversity in the Delta. Understanding how cyanobacterial species will respond to changing environmental conditions in the Delta will help improve cyanoHAB predictions under future water management or hydrologic scenarios.

Authors

• Vivian Klotz*^†, California Department of Water Resources, vivian.klotz@water.ca.gov
• Andreja Kust, Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA and Innovative Genomics Institute, University of California, Berkeley, CA, USA
• Keith Bouma-Gregson, U.S. Geological Survey, California Water Science Center, Sacramento, CA, USA
• Theodore M. Flynn, Division of Integrated Science and Engineering, California Department of Water Resources, West Sacramento, CA, USA
• Judy Westrick, Lumigen Instrument Center, Department of Chemistry, Wayne University, Detroit, MI, USA
• Nicholas Peraino, Lumigen Instrument Center, Department of Chemistry, Wayne University, Detroit, MI, USA
• Spencer Diamond, Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA and Innovative Genomics Institute, University of California, Berkeley, CA, USA
• Jillian F. Banfield, Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA, Innovative Genomics Institute, University of California, Berkeley, CA, USA, Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA and Monash University, Melbourne, Victoria, Australia

*Presenting author, ^†Early Career Award candidate

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Abstract

Primary productivity is an important measure of how much energy is available in an ecosystem. Unfortunately, methods for quantifying primary productivity have previously been costly and time consuming, often leading to this measurement being left out of monitoring programs. However, new advancements in Active Chlorophyll Fluorescence (ACF) methods have emerged as a time and cost-effective method of quantifying phytoplankton primary productivity. Previously, ACF methods have primarily been used in the ocean, an environment with low concentrations of suspended sediment and phytoplankton. Despite more optically complex waters in estuarine environments, such as the Sacramento-San Joaquin Delta (Delta), our results show that this instrument can be applied in these settings. We were able to utilize ACF methods with a labSTAF (Single Turnover Active Fluorometry) instrument. The labSTAF allows for rapid, noninvasive measurements of primary productivity that can be correlated with other mapping data to better understand seasonal, regional, and tidal influences on phytoplankton primary productivity in the Delta. In 2024, the U.S. Geological Survey utilized the labSTAF instrument four times, twice in April and twice in October. It was run alongside discrete sampling and the Boat Based Flow Through System which can measure different water quality parameters, such as chlorophyll, dissolved oxygen, pH, and turbidity. Preliminary results show that photosynthesis is more efficient during spring. We will further investigate STAF measurements to improve monitoring efforts and understand changes in primary productivity.

Authors

• Zoё Siman-Tov*^†, U.S. Geological Survey, zsiman-tov@usgs.gov
• Keith Bouma-Gregson, U.S. Geological Survey
• Jacob Brinkman, U.S. Geological Survey
• Katy O’Donnell, U.S. Geological Survey

*Presenting author, ^†Early Career Award candidate

Abstract

Estimating the passage of out-migrating juvenile Chinook salmon from the Sacramento River to the Sacramento- San Joaquin Delta has played a large role with the rotary screw trapping within the Central Valley to understand the population dynamics of resident salmonids. A key factor in developing passage estimates for salmonids is understanding how efficient a project is within the aquatic system. The Knights Landing rotary screw trap project has conducted over 25 years of efficiency data for Chinook salmon to develop passage estimates. VIE (Visible Implant Elastomer) tagging and whole body dying with BBY (Bismarck Brown Y) groups of juvenile salmonids between 500-3000 were released for mark and recapture to create trap efficiency estimates. Main stem rotary screw trapping projects present many difficulties in creating relevant efficiency estimates compared to smaller tributary projects due to increased flow, consistency in sampling periods, and abundance of salmonids to sample. This presentation highlights the findings of the Knights Landing rotary screw trap efficiency estimates over the duration of the project beginning in 1995, as well as comparing similar projects efficiency data to understand the pitfalls of main stem trap efficiency trials.

Authors

• Corey Fernandez*, California Department of Fish and Wildlife, Corey.Fernandez@wildlife.ca.gov
• Nick Bauer, California Department of Fish and Wildlife

*Presenting author

Abstract

Since the completion of Shasta Dam, winter-run Chinook salmon have been disconnected from their ancestral home on the McCloud River and subject to population declines which have pushed them towards extinction. To reduce this extinction risk, the Winnemem Wintu Tribe in partnership with federal and state agencies are leading an emergency action to reintroduce winter-run to their ancestral home on the McCloud River. Many factors have likely contributed to the decline of winter-run, including climate change, fragmentation of habitat, and disease. However, the extent of disease associated with pathogen exposure on winter-run is largely unknown. This study aims to advance our knowledge of pathogen exposure and disease risk during the reintroduction of winter-run into the McCloud River above Shasta Reservoir. To do so, we are employing comprehensive environmental monitoring through both water sampling and fish tissue analysis to identify links between reintroduction and pathogen dynamics. A component of this monitoring includes collecting weekly water samples that are being analyzed using molecular methods to detect and quantify a wide range of salmonid pathogens (47 pathogens, including viruses, bacteria, and parasites). This environmental surveillance provides essential data on pathogens present in the habitat and helps to estimate potential exposure levels for winter-run. Complementing this water-based environmental assessment, a winter-run field infection study was conducted, where tissues from juvenile salmon that were reared in the McCloud River were assayed to assess pathogen presence and abundance. This poster will present data on these two pieces of data, and provide a more holistic view of pathogen distribution and disease potential on the McCloud River to inform management strategies for winter-run reintroduction.

Authors

• Emerson Feddor*^†, University of California Davis, efeddor@ucdavis.edu
• Andrea Chandler, University of California Davis
• Abbie Ward, University of California Davis
• Jamie Ward, University of California Davis
• Paloma Herrera-Thomas, University of California Davis
• Matthew Patrick Salvador, University of California Davis
• Amelie Segarra, University of California Davis
• Rachel Johnson, NOAA
• Benjamin Atencio, NOAA
• Miles Daniels, NOAA
• Ken Nichols, U.S. Fish and Wildlife Service

*Presenting author, ^†Early Career Award candidate

Poster image not available. Contact poster author directly.

Abstract

The California Central Valley Steelhead (CVS) is a distinct population of anadromous Rainbow Trout (Oncorhynchus mykiss) that is listed as ‘threatened’ under the Endangered Species Act. Critical information gaps regarding our knowledge of Steelhead demographics and life histories in the Sacramento and San Joaquin River watersheds hinder their effective management and conservation. Here we report on the preliminary results of a new collaboration between the Otolith Geochemistry and Fish Ecology Laboratory at UC Davis, the Norwegian Institute for Nature Research, the US Bureau of Reclamation, and the CA Dept. of Fish and Wildlife. In this project we are utilizing increment and geochemical analyses of archived otoliths (ear stones) from 700 CVS to reconstruct the age structure, growth, and migratory life history of Steelhead from the Upper Sacramento, Feather, American, Tuolumne, Merced, and Stanislaus Rivers. These data will allow us to explore the region-wide variation in the life history of CVS. Our initial findings highlight the value of otoliths in providing age, growth, and migratory information for CVS life history analysis. Annual age of adult CVS was reconstructed using opaque and translucent banding patterns. Daily growth rate of the juvenile part of the otolith was reconstructed from daily increment widths. Life history patterns such as natal origin, migratory phenotype, and maternal phenotype are reconstructed using Strontium isotopes (87Sr/86Sr).

Authors

• Feng Zhao*, Otolith Geochemistry and Fish Ecology Laboratory, University of California Davis, mayzhao@ucdavis.edu
• Malte Willmes, Norwegian Institute for Nature Research, malte.willmes@nina.no
• Erin Ferguson, California Department of Fish and Wildlife, Erin.Ferguson@wildlife.ca.gov
• Lea Koerber, California Department of Fish and Wildlife, Lea.Koerber@wildlife.ca.gov
• Steve Tsao, California Department of Fish and Wildlife, Steve.Tsao@wildlife.ca.gov
• Daniel Martinez, California Department of Fish and Wildlife, Daniel.Martinez@wildlife.ca.gov
• Brian Mahardja, U.S. Bureau of Reclamation, bmahardja@usbr.gov
• Michael Beakes, U.S. Environmental Protection Agency, Beakes.Michael@epa.gov
• Levi Lewis, Otolith Geochemistry and Fish Ecology Laboratory, University of California Davis, lslewis@ucdavis.edu

*Presenting author

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Abstract

Field enclosures have long been used to test how fish respond to habitat conditions. The Department of Water Resources (DWR) began using Delta Smelt enclosures in 2019 to test the ability of cultured smelt to survive and grow in the estuary and test key management questions. These questions include understanding the effects of season, location, hatchery ancestry, supplementation strategies, and managed habitat actions in summer-fall that affect smelt, but we have found that some of these questions can be tested more effectively than others. Here, we focus on summarizing field deployments in summer and fall periods of 2019, 2023, and 2024, designed to test the effectiveness of the Fall X2 and Suisun Marsh Salinity Control Gates managed habitat actions. We contrast fish survival and condition metrics (e.g., condition factor, hepatosomatic index (HSI), liver glycogen, and upper thermal tolerance (CTmax)), where feasible across the three deployment years. We also assess zooplankton and diets of caged fish compared to wild-caught fish during similar time period, when possible. We found >50% survival in all years of caged smelt in summer- fall, with generally higher survival in the Sacramento River at Rio Vista compared to Suisun Marsh. Other metrics such as condition factor, HSI, liver glycogen, and CTmax were influenced by year and location. Together, our findings challenge the hypotheses behind these management actions (with mixed rejection and support) and raise concerns about confounding factors limiting our ability to extend the results of the cage experiments to broader habitat conditions (e.g., biofouling, restricting foraging behavior, and food limitations). Overall, we highlight DWR’s Delta Smelt enclosure program, key findings from deployments, and critical problems that may confound future summer-fall deployments.

Authors

• Brittany Davis*, California Department of Water Resources, Brittany.e.davis@water.ca.gov
• Trishelle Tempel*, California Department of Water Resources
• Christina Burdi, California Department of Water Resources
• Scott Meyer, California Department of Water Resources
• Bruce G Hammock, University of California Davis
• Heather Bell, University of California Davis
• Dennis Cocherell, University of California Davis
• Rosemary Hartman, California Department of Water Resources

*Presenting authors

Abstract

Visible implant elastomer (VIE) tagging is a commonly-used method for marking and monitoring large numbers of cultured fish released into the wild for conservation purposes, such as the supplementation of endangered Delta Smelt. This method is favored for its low-cost materials, rapid processing, and low mortality rates, as well as its high tag retention and detectability under field conditions. The variety of VIE colors available also facilitates batch marking unique groups, which can be used to evaluate the effectiveness of different release methods, locations, and times during ‘experimental releases’ for the Delta Smelt supplementation program, for example. However, the ability to distinguish between batches of released fish depends on the correct assignment of fish to their corresponding tag color (i.e., original release group). We surmised that color vision deficiency (CVD) in humans, a common condition that affects approximately 9% of males and 2% of females worldwide, could influence accuracy of these assignments. To test this, we solicited observers with and without CVD to identify the tag color (blue, green, orange, red, and yellow) of anesthetized, VIE-tagged Delta Smelt from photos and in person. Observers without CVD correctly identified VIE color in 96.8% of photographed fish and 94.8% of fish observed in person, whereas observers with CVD correctly identified VIE color in 60.0% of photographed fish and 43.9% of fish observed in person. For both in-person and photo-based identifications, observers with CVD were most proficient at identifying blue tags (99.0% correct) and least proficient at identifying green (89.9% incorrect) and yellow (88.1% incorrect) tags. We showed that, although CVD reduces the accuracy of VIE-tag-color identification in Delta Smelt, complementary use of high-quality photographs offers a robust, independent means to verify field-based identifications.

Authors

• Carissa Long*, U.S. Fish and Wildlife Service, carissa_long@fws.gov
• Yi-Jiun Jean Tsai, U.S. Fish and Wildlife Service
• Gonzalo C. Castillo, U.S. Fish and Wildlife Service
• Tien-Chien Hung, U.S. Fish and Wildlife Service
• Vanessa D. Tobias, U.S. Fish and Wildlife Service
• Evan W. Carson, U.S. Fish and Wildlife Service

*Presenting author

Abstract

The Delta Smelt, endemic to the San Francisco Estuary and Sacramento-San Joaquin Delta, is an endangered species on the brink of extinction. Understanding how these fish utilize habitats and respond to environmental variation is important for implementing and assessing the effectiveness of conservation efforts. Since wild Delta Smelt are rarely encountered, controlled enclosure experiments seek to assess fish response over time using hatchery raised individuals. However, one of the challenges of working with Delta Smelt is that they are sensitive to physical handling resulting in an acute stress response, often with direct or delayed mortality. This precludes multiple measurements of an individual needed for calculating growth rates and necessitates the use of apparent population growth rates which include excessive inherent variability. To avoid this undesired outcome and improve growth assessments at multiple points in a fish’s life, we developed a non-contact approach to measuring Delta Smelt size and condition. The approach was adapted from a method developed by Holmes and Jeffres (2020) on juvenile Chinook Salmon. The process involves collecting oblique fish images in a narrow aquarium, manual landmark digitization, and regression of the resulting truss network measurements to estimate a fish’s length, weight, and condition. The method proved to be precise with a mean absolute percent error (MAPE) of 3.37% and a mean absolute error (MAE) of 0.07g, and unbiased with distributions centered around 0. This method can be performed on an unstable platform, such as a boat, where traditional weight measurements are prohibitive. This method has the potential for inclusion in fish sampling workflows for various species where accurate size and condition information is desired and where minimal handling of sensitive and imperiled fish species is needed.

Authors

• Eric Holmes*, California Department of Water Resources, eric.holmes@water.ca.gov
• Mackenzie Miner, California Department of Water Resources
• Alexa Camilleri Evans, California Department of Water Resources
• Amanda Niemela, California Department of Water Resources
• Francheska Torres, California Department of Water Resources

*Presenting author

Abstract

This study presents the first comprehensive investigation of sperm morphology in three smelt species in California: the endangered delta smelt (Hypomesus transpacificus), the threatened longfin smelt (Spirinchus thaleichthys), and the introduced wakasagi (H. nipponensis). We analyzed the ultrastructure of their spermatozoa, focusing on the head length, head width, head area, midpiece length, flagellum length, and total sperm length using Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM). SEM images revealed that all three species share a rounded sperm head with a short midpiece connecting to the flagellum, as in most teleosts. For delta smelt, average measurements for sperm head length, head width, head area, midpiece length, flagellum length, and total sperm length were 1.61 ± 0.16 μm, 1.03 ± 0.08 μm, 1.34 ± 0.23 μm², 0.75 ± 0.16 μm, 27.41 ± 3.97 μm, and 29.39 ± 4.19 μm, respectively. In longfin smelt, these measurements were 1.63 ± 0.16 μm, 1.01 ± 0.07 μm, 1.32 ± 0.15 μm², 0.83 ± 0.16 μm, 30.46 ± 3.93 μm, and 32.13 ± 4.38 μm. Wakasagi sperm had averages of 1.65 ± 0.10 μm, 0.98 ± 0.07 μm, 1.32 ± 0.13 μm², 0.82 ± 0.11 μm, 31.57 ± 4.66 μm, and 33.80 ± 4.50 μm. TEM analysis highlighted critical internal features of the midpiece, including the centrioles, nucleolus, and surrounding nuclear envelope. It also showed the presence of proximal and distal centrioles, with the flagellum connected to the distal centriole. The typical nine peripheral doublets and two central microtubules (9+2) of flagellum was also clearly visible. This pioneering study fills a significant knowledge gap by detailing the sperm morphology of these smelt species, providing a foundation for future reproductive research and potential conservation efforts.

Authors

• M. Moshuir Rahman*, Department of Biological and Agricultural Engineering, University of California Davis, momrahman@ucdavis.edu
• Ferisca Putri, Department of Biological and Agricultural Engineering, University of California Davis
• Tien-Chieh Hung, Department of Biological and Agricultural Engineering, University of California Davis

*Presenting author

Abstract

Suisun Bay and Suisun Marsh, especially Montezuma Slough, are historically important habitat for endangered Delta Smelt (Hypomesus transpacificus) and other fishes in the San Francisco Estuary (SFE). The Suisun Marsh Salinity Control Gates (SMSCG) in eastern Montezuma Slough are typically operated in the fall to increase low salinity habitat in Suisun Marsh to benefit waterfowl. In 2018, the gates were operated in August to potentially benefit Delta Smelt by increasing low salinity habitat during the summer, as outlined in the Delta Smelt Resiliency Strategy. The gates were opened during ebb tides and closed during flood tides to maintain fresh water in Montezuma Slough. During this time, the California Department of Fish and Wildlife (CDFW) added additional zooplankton monitoring from July to October to examine the effect of gate operations on the zooplankton community. This zooplankton data, coupled with fish collected by routine CDFW and U.S. Fish and Wildlife Service surveys, gives us the opportunity to determine the effect of augmented flow (via SMSCG operation) on fish diets and prey selectivity in the SFE. The CDFW Diet and Condition Study examined the diets of Delta Smelt and other co-occurring fish—Longfin Smelt (Spirinchus thaleichthys), Striped Bass (Morone saxatilis), American Shad (Alosa sapidissima), and Threadfin Shad (Dorosoma petenense)—found within the SMSCG footprint from Suisun Bay to the lower Sacramento River. We compared fish diets during the SMSCG action in 2018 to those in 2019, a non-action wet year. This study not only allows for comparisons of fish diets during the SMSCG management action but also adds valuable information about dietary overlap between native and invasive species, prey selectivity, as well as information on the previously unknown diets of fish species in the SFE—all of which will inform management decisions aimed at increasing beneficial habitat and prey availability for native fishes.

Authors

• Nene Ugbah*^†, California Department of Fish and Wildlife, Nene.Ugbah@wildlife.ca.gov
• Christina Burdi, Department of Water Resources
• Spencer Breining-Aday, California Department of Fish and Wildlife

*Presenting author, ^†Early Career Award candidate

Abstract

The genetically distinct population of Longfin Smelt (Spirinchus thaleichthys) in the San Francisco Estuary (SFE) has experienced significant population declines in recent decades, resulting in an increased risk of extinction. The effectiveness of conservation strategies for this species hinges on the development of robust population models and culture methods, which rely on accurate parameter estimates for age-at-maturity, size-at-maturity, and size-specific fecundity. Here, we summarize ontogenetic, temporal, and spatial patterns in maturation and fecundity of wild Longfin Smelt collected across the SFE over the last two decades. We also summarize size-independent age estimations, generated via otolith-based aging methods, which allow for better distinction among age-1, age-2, and age-3 fish. The gonadosomatic index (GSI) of Longfin Smelt increased sharply above 60 mm standard length (SL), and over 50% of fish over 70 mm SL were found to contain gonads with either fully mature oocytes or oocytes approaching full maturity. Clutch fecundity averaged ~5000 eggs per female, but could potentially range to >15,000. These findings are key to future conservation efforts such as UC Davis’s fledgling Longfin Smelt Conservation and Culture Program.

Authors

• Nikolas Floros*^†, University of California Davis, njfloros@ucdavis.edu
• Sami Araya, University of California Davis
• Alejandro Lama, University of California Davis
• Brian Alper, University of California Davis
• Alexander Scott, University of California Santa Cruz
• James Hobbs, University of California Davis
• Levi S. Lewis, University of California Davis

*Presenting author, ^†Early Career Award candidate