2024 IEP Workshop Poster Exhibits

No poster image available.

Abstract

Replacing paper-based data entry systems with electronic data collection for field research is gaining popularity. Direct digital data entry in the field is potentially cheaper and faster but less accurate than entering data from paper datasheets into a computer. We conducted a pilot study in the fall and winter of 2023 to investigate the costs and benefits of field data entry using digital data sheets versus office data entry using paper data sheets. We analyzed data for four long-term fish monitoring surveys in the Sacramento-San Joaquin Delta conducted by the U.S. Fish and Wildlife Service – the Delta Juvenile Fish Monitoring Program’s (DJFMP) beach seine, midwater trawl, and electrofishing surveys and the Enhanced Delta Smelt Monitoring Program’s (EDSM) Kodiak trawl survey. Results are forthcoming.

Authors

• Adriana Arrambide*, USFWS, adriana_arrambide@fws.gov
• Cook, John (Ryan) USFWS
• Erly, Kate USFWS
• Higginson, Paula E USFWS
• Hope, Trevor M USFWS
• Huber, Eric R USFWS
• Macfarlane, Claudia M USFWS
• Santana, Gabriel USFWS
• Speegle, Jonathan USFWS

* Presenting Author

Abstract

Interagency monitoring efforts are a pathway to improve field efficiency and reduce the heavy lift of monitoring programs. However, managing the data in a cohesive and accessible manner for all contributing partners and interested parties can quickly become slow and convoluted.

The Fish Restoration Program (FRP) seeks to share a data management approach for situations where groups generate and maintain separate portions of a dataset. The FRP continuous water quality dataset is collected by two departments, CDFW and DWR, and comes from over 10 water quality stations within tidal habitat restoration sites – making the need for a shared, semi-automated data pipeline a top priority.

Through upgrades to electronic data sheets, biweekly meetings, and R code managed within GitHub, FRP has developed a data pipeline that can be accessed, updated, and managed by either department. Outcomes from this effort include faster responses to data requests, regular processing of data, and increased time for data analysis.

As a final component to the data pipeline, FRP has developed improved data visualizations for general use by the broader Program and for improved management of/response to station conditions.

Authors

• Emma Mendonsa*, DWR, Emma.mendonsa@water.ca.gov
• Daniel Cox, CDFW
• Brian Armstrong, DWR

*Presenting author

Abstract

Fishery independent monitoring in the San Francisco Estuary (SFE) includes extensive survey coverage by the many trawl- and seine-based surveys of the Interagency Ecological Program (IEP). These surveys primarily sample small and/or juvenile fishes due to the relatively small net dimensions and tow speeds. As a result, the adult component of many SFE fish species was not well sampled, representing a shortcoming in the IEP’s ability to track changes in age-structured regional fish assemblages. Through the addition of a new study to the IEP workplan, called the “Enhanced Large Fish Study” (ELFS), we aim to fill this knowledge gap and contribute to the California Department of Water Resource’s compliance with State Water Resource Control Board Decision 1641 for the operation of the State Water Project.

In spring of 2023, we piloted the first field season of the ELFS, employing American Fisheries Society experimental gillnets in a stratified random sampling design in the North Delta and Lower Sacramento River corridor. In total, we set 153 approximately one-hour gillnet sets over 25 sampling days, including 33 paired day and night sets to test diurnal effects on catch. We caught a total of 16 fish species of which five were native and 11 were non-native, ranging in size between 101mm and 678mm fork length. This season proved the efficacy of using experimental gillnets to sample the large fish community within portions of the SFE. Future sampling years will include coordinated sampling with the US Fish and Wildlife Service Delta Boat Electrofishing Survey and an expansion into downstream habitats including Suisun Bay and Marsh.

Authors

• Taryn Mitoma*⁺, UC Davis, tbmitoma@ucdavis.edu
• Dylan K. Stompe, CDFW Region 3
• Analicia Ortega⁺, CDFW Region 3
• James A. Hobbs, CDFW Region 3

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Habitat parameters can influence the reproductive success and survival of native and non-native fish. The California Sacramento-San Joaquin Delta system has undergone alterations to its water system over the years, specifically changes in flow and water quality parameters. There is a pressing need to understand how species occurrence, diversity, and interactions are influenced by water management and climate change. Our research looks to explore key habitat quality factors (bottom depth, temperature, dissolved oxygen, salinity, and turbidity) and their relationships with native vs. non-native larval fish species abundance in the Sacramento-San Joaquin Delta system. The U.S. Fish and Wildlife Service Enhanced Delta Smelt Monitoring Program has used a 20mm larval trawl net to collect larval fish assemblage data from 2017 through 2023. By utilizing this larval trawl data, we aim to uncover any patterns underlying the presence of native vs non-native larval fish, based on the regional differences in water quality conditions.

Authors

• Trevor Hope*⁺, Lodi U.S. Fish and Wildlife Service, trevor_hope@fws.gov
• Gabriela Garcia*⁺, Lodi U.S. Fish and Wildlife Service
• Claudia Macfarlane*⁺, Lodi U.S. Fish and Wildlife Service

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

The California Department of Fish and Wildlife’s (CDFW) Native Fishes Unit (NFU) conducts the Smelt Larva Survey and 20-mm Survey to monitor the distribution and relative abundance of larval and juvenile Longfin Smelt (Spirinchus thaleichthys) and Delta Smelt (Hypomesus transpacificus). These surveys provide data to water managers to assess the risk of entrainment of these species into the water export facilities. While these surveys focus on Osmerids, there are other species of concern amongst the catch, including white sturgeon (Acipenser transmontanus). These anadromous fish are found from Gulf of Alaska to Monterey Bay. Locally, white sturgeon larvae are typically found in the upper Sacramento River (Wang et al., 2010). Within our surveys, larvae and juvenile abundance fluctuate yearly. During dry years only a few individuals are collected compared to wet years where the number of white sturgeon collected increases exponentially. Concern for white sturgeon increased due to the reoccurrence of harmful algal blooms in the San Francisco Bay estuary, decreasing habitat, and historic overfishing. The presence of white sturgeon larvae in the most recent NFU surveys generated questions on how this species is coping with changing water years and water conditions. In this study, we collected data from various CDFW surveys within the San Francisco Bay Estuary, such as San Francisco Bay Study, Native Fish unit, and Young Fish Investigations Unit, to examine the historical trends of young white sturgeon. We compared this data to annual precipitation levels and flow data for the last 20 years. We expect higher precipitation and flow years to increase available habitat suitable for larval white sturgeon rearing. This would increase the amount of white sturgeon seen in our surveys. These results provide insight of how white sturgeon populations correlate with yearly precipitation and flow. Understanding how white sturgeon larvae survive in fluctuating hydrology patterns can help inform conservation decisions.

Authors

• Tariq Celeste CDFW
• Jorge Chagoya*⁺, Jorge.Chagoya@wildlife.ca.gov
• Liz Lorz CFDW

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Detecting DNA in the environment (eDNA) from aquatic species is a non-invasive and cost-effective method of monitoring vulnerable species and is a valuable addition to the resource management toolbox. Quantitative PCR (qPCR) is currently the leading technique for aquatic eDNA detection. However, processing samples via qPCR requires expensive instrumentation, molecular biology experience, and several hours of benchwork to produce results. Outsourcing to laboratories with the necessary equipment can further increase waiting times for results. Recent advances in CRISPR-based diagnostics have enabled the development of alternative methods for eDNA detection. Specific High-sensitivity Enzymatic Reporter unLOCKing (SHERLOCK) assays use the CRISPR-Cas13a enzyme complex to detect target nucleic acids and produce a fluorescent signal. These assays are rapid (< 1 hr), sensitive, and can be performed by non-experts with inexpensive equipment under field conditions. Multiple such assays have been developed for rapid detection of aquatic species in California water bodies. We developed a SHERLOCK assay to monitor Chinook Salmon (Oncorhynchus tshawytscha) in western North America. We designed RPA primers and a crRNA guide sequence to target a species-specific region of the Cytochrome c oxidase subunit III (COIII) gene in Chinook Salmon mitochondrial DNA. The RPA primers duplicate the target region, if present, in an eDNA sample. The crRNA complements the target site and programs the CRISPR-Cas13a complex to activate when the target region is detected in an eDNA sample. These two factors contribute to high specificity in SHERLOCK assays. Our final assay detected tissue-derived DNA from 40 Chinook Salmon individuals from multiple populations within 30 minutes of SHERLOCK reaction initiation. We tested specificity using tissue-derived DNA from eight salmonid species that co-occur with Chinook Salmon. With further refining, we anticipate that our assay will be useful for Chinook Salmon detection across their current range.

Authors

• Diana Muñoz*⁺, Genomic Variation Laboratory, University of California, Davis, CA damunoz@ucdavis.edu
• Emily Funk, Genomic Variation Laboratory, University of California, Davis. CA
• Andrea Schreier, Genomic Variation Laboratory, University of California, Davis, CA
• Ryan Kelly, School of Marine and Environmental Affairs, University of Washington, Seattle, WA

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Delta Smelt are a mostly annual species and face various stressors such as food limitation and contaminants which can impair reproduction. Using adult fish caught from 2011 to 2018 from November to May, we examined morphometric indicators (gill pathology and liver lesions), nutritional indicators (histopathologically estimated liver glycogen depletion), and physical condition (fork length and condition factor) in relation to reproductive metrics (gonadosomatic indices/GSI, fecundity, and oocyte weight) to determine if nutritional and contaminant stressors are influencing Delta Smelt reproduction. Fork length and condition factor had the strongest positive relationship with reproductive metrics. Unexpectedly, more severe glycogen depletion was associated with higher oocyte mass, and higher GSI. Gill and liver lesion severity had a negative relationship with GSI. When examining changes to physical condition, morphometric indicators, nutritional indicators, and reproductive metrics across the study years there was no clear pattern related to water year. Contaminants appear to have a negative effect on Delta Smelt reproduction; however, reproductive success appears to be primarily influenced by factors that vary on different time scales. For example, fork length and condition factor are determined by conditions an individual experiences over its life span, while the importance of liver glycogen indicates shorter term storage of energy needed for oocyte production. These factors suggest prey are important to support growth and reproduction; females need sufficient nutrition to grow and store glycogen store oocyte production.

Authors

• Calvin Akiyama Lee*, ICF Calvin.AkiyamaLee@icf.com
• April Smith, ICF
• Shawn Acuña, MWD
• Bruce Hammock, UC Davis
• Jason Hassrick, ICF
• Swee Teh, UC Davis

* Presenting author

Abstract

Delta Smelt (Hypomesus transpacificus) conservation efforts have shifted towards culture methods in recent years due to a lack of wild spawning stocks. Distinguishing between wild and hatchery-raised fish is vital for establishing effective management practices, however current differentiation methods (i.e., fin clips, fluorescent dyes, otolith chemical signatures) are time consuming and provide minimal information of the origin of the fish. Otoliths may provide a solution to this problem, by allowing for the development of batch-tagging techniques. Otoliths provide a metabolically inert record of growth fluctuations, which can come about in response to stress from rapid changes in environmental conditions. Here, we are working with DWR and the FCCL at UC Davis to develop and test otolith-based batch-marking techniques. Larval Delta Smelt were exposed to 3 different treatments: temperature fluctuations (“thermal bar-coding”), salinity fluctuations (geochemical tagging), and a control treatment. Otolith marking treatments were imposed at 42 days-post-hatch (dph) and 86 dph, with all fish euthanized at 127 dph. Afterwards, 30 fish were selected from each treatment for otolith analysis. Otoliths were dissected and sectioned sagittally, allowing for optimal clarity of daily increments. Otoliths were then examined visually and geochemically (LA-ICP-MS) to assess the presence and timing of thermal check marks (temperature treatment) and geochemical spikes (salinity treatment), respectively, with each treatment contrasted with the control group. Patterns and shapes of otoliths were also contrasted with those observed in wild-caught Delta Smelt. These otolith-based batch-marking techniques provide a new and economical method for tagging large quantities of supplemental Delta Smelt, allowing for the identification and analysis of the success of growth and survival of Delta Smelt to inform supplementation and other population recovery efforts.

Authors

• Brian Alper*⁺, UC Davis, baalper@ucdavis.edu
• Levi Lewis, UC Davis
• Tien-Chieh Hung, UC Davis
• Luke Ellison, UC Davis
• Troy Stevenson, UC Davis
• Trishelle Tempel, California Department of Water Resources

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Delta Smelt (Hypomesus transpacificus) predominantly inhabit the freshwater and low salinity regions (i.e., 0.5 to 6 psu) of the Sacramento-San Joaquin Delta and San Francisco Estuary. With a complex life history encompassing freshwater residency, brackish water residency, and migration, understanding the specie’s response to salinity variations across its migratory life cycle is crucial. While previous studies have examined salinity’s influence on recent growth and physiological parameters, a comprehensive investigation spanning the entire life cycle is lacking. In this study, we utilized joint otolith geochemical and increment profiles to explore the ontogenetic variation in daily growth of individual Delta Smelt in relation to daily ambient salinity fluctuations. Otoliths from 165 juvenile Delta Smelt were collected from various agency archives across the San Francisco Estuary. Daily growth chronologies were aligned with daily reconstructed salinities using a Sr-isotope-to-salinity mixing model. Generalized additive models (GAMs) were employed to examine the interactive effects of salinity and ontogeny on Delta Smelt growth. Our findings reveal that Delta Smelt larvae up to 50 days old exhibit suboptimal growth beyond a salinity threshold of approximately 3 psu, indicating vulnerability to slight changes in ambient salinity during early life-stages. However, juveniles and subadults demonstrate robust growth in salinities up to 6 psu. By elucidating the growth-salinity relationships across the species’ life history in wild-collected specimens, our study enhances our understanding of the ecological dynamics of Delta Smelt populations and provides valuable insights for current conservation and population management strategies.

Authors

• Brian Alper*⁺, UC Davis, baalper@ucdavis.edu
• Levi Lewis, UC Davis
• Tien-Chieh Hung, UC Davis
• Luke Ellison, UC Davis
• Troy Stevenson, UC Davis
• Trishelle Tempel, California Department of Water Resources

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Delta Smelt cultured at the Fish Conservation and Culture Laboratory are reared in multi-family groups at specific densities that vary depending on life stage. This strategy has successfully produced generations of Delta Smelt for the refuge population, but is labor intensive; for maintenance, staff count and cull fish approximately every 40 days until adulthood to maintain proper densities and tag all adults to track parentage. Also, with this rearing strategy, there is a risk that individual families could be lost due to competition within multi-family groups. Thus, developing more efficient culture protocols that mitigate these issues would benefit Delta Smelt production.

One proposed strategy is to rear Delta Smelt in single-family groups without density limits, in which each family is cultured separately, with reduced counting benchmarks, and without culling during younger life stages. To determine the effects of such a strategy, we reared Delta Smelt from 0 to 198 days post-hatch (dph) in single-family groups using smaller tanks than normal (to compensate for fewer fish per group) and without culling. We measured larvae for length and weight at 40, 80, 168, and 196 dph. We found that initial stocking density at 0 dph was negatively correlated with size at 40 and 80 dph, but was not correlated at 168 or 196 dph. We also found that fish reared under experimental conditions did not differ in size compared to those reared under normal, density-controlled conditions for the refuge population at 40 dph. However, experimental fish were smaller than refuge fish at 80, 168, and 196 dph. These results suggest that high stocking densities may stunt growth during early life stages and that this size effect becomes apparent during later life stages.

Authors

• Yi-Jiun Jean Tsai*, UC Davis, yjtsai@ucdavis.edu
• Luke Ellison, UC Davis
• Troy Stevenson, UC Davis
• Tien-Chieh Hung, UC Davis

* Presenting author

Abstract

Fish movement and survival are key metrics for evaluating the success of supplementary releases of cultured Delta Smelt. In addition to net sampling, acoustic telemetry offers an independent and non-lethal way to gather course-scale information on survival, movement, and distribution, as well as fine-scale information on habitat use and movement behavior under various water operation scenarios. Prior to implementing acoustic tagging of Delta Smelt in natural waterways, it is imperative to understand whether the tagging process negatively affects fish health and performance. Using cultured adult Delta Smelt (mean FL = 79.1 mm, SD = 6.7) we evaluated whether a newly miniaturized acoustic transmitter (0.06g) can be implanted while minimizing effects on survival and swimming ability. We also explored potential improvements to handling and tagging techniques by evaluating survival and tag retention at two tagging locations (ventral and lateral incisions) and two water temperatures (12 and 16°C). Thirty days after tagging, survival in the surgical groups was higher than in the previous study (Wilder et al. 2016) which utilized a larger acoustic tag (0.22 g). Most mortalities occurred in the first three to eight days post-tagging. There was not a marked difference in survival between the tag implantation locations, nor did water temperature affect mortality rates. Experiments are ongoing to further improve survival by identifying a more resilient life-stage for tagging. We will also test sublethal effects of tagging, such as changes in behavior and swimming capacity. Ultimately, these data will refine handling and surgical procedures so that tagging effects are minimized in the field. Improved understanding of Delta Smelt movement behavior, survival, and habitat use in natural waterways will be key for recovering this critically endangered species.

Authors

• Sebastian Gonzales*⁺, Department of Wildlife, Fish, and Conservation Biology; University of California Davis, sggonzales@ucdavis.edu
• Eric Chapman, ICF
• Anna Steel, Department of Wildlife, Fish, and Conservation Biology, University of California, Davis
• Jason Hassrick, ICF
• Daniel Deng, Pacific Northwest National Labs
• Rick Wilder, ICF
• Nann A. Fangue, Department of Wildlife, Fish, and Conservation Biology, University of California, Davis

* Presenting author
⁺ Early Career Award candidate

Abstract

The environmental conditions in the San Francisco Estuary have led to declines in native fish populations since long-term monitoring began in the 1950s. While the wide range of monitoring studies in the region effectively identifies trends in relative abundance, it is harder to evaluate the effects of these conditions on fish habits. Longfin smelt (Spirinchus thaleichthys) is a listed native fish species experiencing a population decline in the estuary. The San Francisco Bay Study covers much of their range in the estuary containing a pelagic and benthic trawl. We show that catch rates by the survey’s paired trawls have been diverging over the past 2 decades, as the midwater trawl catch rate shows a steeper decline than the bottom trawl rate.

We analyzed the Bay Study catch of juvenile longfin smelt since 1980 using generalized linear modeling to identify possible causes of this divergence, such as environmental factors or the potential for changes to the sampling protocols. We observed that Secchi depth in the estuary has increased by an average of 20-centimeters. This decline in turbidity is also linked to increasing depth in much of the estuary.

These trends coincide with a vertical shift in distribution of juvenile longfin smelt deeper into the water column.  These results suggest that in clear water with low attenuation, longfin smelt may find refuge from predators in the darker depths.

The paired sampling design of the San Francisco Bay Study provides a unique opportunity to evaluate the role that changes in vertical distribution may have in biasing estimates of relative abundance in monitoring surveys. As longfin smelt become more bottom oriented, long-term midwater trawl data may underestimate the population size while bottom trawl data may overestimate the population size.

Authors

• Andrew Kalmbach*, ICF, andrew.kalmbach@icf.com
• Shawn Acuna, Metropolitan Water District
• Jason Hassrick, ICF

*Presenting author

Abstract

Delta Smelt (Hypomesus transpacificus) is a critically endangered migratory fish that is endemic to the San Francisco Estuary. Most Delta Smelt are believed to reproduce at 1 year of age; however, length data from field surveys suggest the historic presence of big, old, fat, fecund females (BOFFFs in the fisheries literature) that deviate from this pattern and may spawn at age 2. These older females likely exhibit higher fecundity than age-1 spawners, thus possibly contributing disproportionately to population dynamics. Yet, it remains unclear whether these large females are truly age-2 or fast-growing age-1 fish. Here, opaque and translucent (“annual”) banding patterns in otoliths (calcified ear stones) were used to reconstruct the annual ages of Delta Smelt from the California Department of Fish and Wildlife’s (CDFW) Spring Kodiak Trawl Survey (2003 to 2023). Although rare, otolith-based analyses identified several large individuals that indeed survived a full second summer and were possibly preparing to spawn in their second year of life. Our results confirm the presence of this longer-lived life-history phenotype and suggest that variation in the abundance of age-2 spawners could be an important parameter for an improved understanding of the biology and conservation of this imperiled species.

Authors

• Claire Chung*⁺, UC Davis, cychung@ucdavis.edu
• Alon Robbins, UC Davis
• Levi Lewis, UC Davis
• Jim Hobbs, CDFW
• Swee Teh, UC Davis
• Bruce Hammock, UC Davis

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

The Genetics Monitoring Laboratory at the Department of Water Resources, Division of Integrated Science and Engineering is utilizing cutting-edge genetic monitoring methods to fulfill high-priority 2020 Incidental Take Permit (ITP) mandates pertaining to the continued operation of the State Water Project. One such method, referred to as SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing), is a reaction that uses CRISPR-Cas13a to provide rapid genetic identification from biological samples and is an essential tool for multiple mandate-fulfilling projects. Many of these projects require interagency collaboration to support genetic monitoring of endangered fish species in the Sacramento-San Joaquin Delta and will provide accurate and fast genetic results to support decision management. Through this presentation, I aim to describe the steps associated with the SHERLOCK process and highlight key genetic monitoring projects where the applied use of SHERLOCK is invaluable.

Authors

• Ross Harper*⁺, Department of Water Resources, ross.harper@water.ca.gov
• Melinda Baerwald, Department of Water Resources
• Daphne Gille, Department of Water Resources
• Sarah Brown, Department of Water Resources

* Presenting author
⁺ Early Career Award candidate

Abstract

Genetic-based species identification is an essential tool for managers in the San Francisco Bay-Delta. Methods leveraging species-specific DNA patterns can distinguish between morphologically similar organisms, for example between the endangered Delta Smelt (Hypomesus transpacificus) and the non-native Wakasagi (Hypomesus nipponensis). Although these methods provide unambiguous species identification, until recently they could only be performed in a small number of specialized genetics laboratories, resulting in a delay in obtaining timely data for management decision-making. Here we describe the collaborative implementation of SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) between UC Davis researchers and agency scientists at the US Fish and Wildlife Service - Lodi Fish and Wildlife Office. The SHERLOCK method is rapid, easy to perform, and can use non-invasively sampled mucus swabs from individual fishes. The assay materials require only a small footprint in existing laboratory spaces, and the detection instrument is semi-portable and can be stored out of the laboratory when not being used if space is limited. In our presentation we will provide an overview of the protocol, infrastructure, and other considerations needed for SHERLOCK implementation at a government agency laboratory with no previous experience with in-house genetic identification. We will also present preliminary SHERLOCK species identification results for Delta Smelt swab samples collected by the Enhanced Delta Smelt Monitoring (EDSM) program during late 2023-early 2024, including summarizing the data and highlighting any technical challenges encountered during the current pilot phase implementation. Finally, we will provide general guidance on best practices for SHERLOCK implementation and highlight additional applications beyond smelt species identification. Implementing SHERLOCK at agency laboratories will ultimately improve turnaround time for producing data critical to management decisions and accelerate progress towards the long-term goal of making the technology accessible to all Bay-Delta scientists.

Authors

• Natalie Kolm*⁺, Genomic Variation Laboratory, Department of Animal Science University of California, Davis; nkolm@ucdavis.edu
• Ravi Nagarajan, Genomic Variation Laboratory, Department of Animal Science University of California, Davis
• Ryan Cook, U.S. Fish and Wildlife Service, Lodi, CA
• Denise Goodman, U.S. Fish and Wildlife Service, Lodi, CA
• Brian Mahardja, US Bureau of Reclamation, Sacramento, CA
• Taylor Senegal, U.S. Fish and Wildlife Service, Lodi, CA
• Andrea Schreier, Genomic Variation Laboratory, Department of Animal Science University of California, Davis

* Presenting author
⁺ Early Career Award candidate

Abstract

Conservation implementation by the U.S. Fish and Wildlife Service can benefit from knowing where a listed species may be distributed, and what habitat features and areas are essential to conserving a species. For the Bay-Delta Distinct Population Segment of Longfin Smelt (Spirinchus thaleichthys), many of these key physical and biological parameters are only ephemerally present in the dynamic San Francisco Estuary. The locations of these features, such as favorable salinity, temperature, and turbidity can shift substantially in the estuary depending on freshwater outflow. This geographic variability presents challenges when attempting to delineate a static distribution of a key lifestage, such as spawning adults and rearing larvae. To determine Bay-Delta Longfin Smelt larval and post-larval distribution under a broad range of conditions and year types, we focused on hydrologic processes for transport and retention in the low salinity zone. Using X2 as an approximation of favorable larval habitat we examined the historical distribution of X2 during January through May (when larvae are present and require low salinity habitat) over nine decades. We then fit a series of GAMs examining the geographic distribution of larvae and potential spawners throughout the year using data from multiple long-term monitoring surveys. We compared the results of the GAMs with the historical distribution of X2 to inform our mapping exercise. This quantitative approach produced an area with clear boundaries that are protective of the spawning and rearing population. This method for projecting the DPS’ distribution of this key lifestage averaged across space and time should be useful for the public, natural resource managers, and biologists who may be engaged in Longfin Smelt conservation. It should be noted that this exercise cannot replace more focused, temporally contextual distribution predictions in any given set of physical and biological conditions extant within any specific hydrological and population context.

Authors

• Joseph Miller*⁺ USFWS Bay-Delta Fish and Wildlife Office, joseph_miller@fws.gov
• Vanessa Tobias, USFWS Lodi Fish and Wildlife Office
• Steven Detwiler, USFWS Bay-Delta Fish and Wildlife Office

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

A statistical model of total monthly juvenile salmonids salvage at State Water Project (SWP) and Central Valley Project (CVP) export facilities was developed by multiple linear regression using 2008-2018 WY. The explanatory variables included the combined SWP/CVP monthly export pumping along with Delta inflows from tributaries that are sources of salmonids entering the interior Delta. These tributaries included the Sacramento (SAC), San Joaquin River at Vernalis (SJR), Mokelumne River flow at Woodbridge (MOKE), Cosumnes River at Michigan Bar (CSMR) and other minor eastside tributaries. The DSSM also included flows into Georgianna Slough-Delta Cross Channel (GS-DCC), Old and Middle River (OMR) flows and X2 salinity as indicators of interior Delta flow conditions contributing to entrainment of salmonids at the SWP and CVP fish salvage facilities.

Now, I plan to use the post 2018 WY explanatory data as inputs to the existing DSSM model to analyze how well model matches 2019-2023 WY salvage data.

Authors

• Márcia Scavone-Tansey* – DWR, Marcia.Scavone-Tansey@water.ca.gov

* Presenting author

No poster image available.

Abstract

Efforts to monitor and protect rare and listed species, such as Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys), are often limited by the accuracy and efficiency of sampling techniques. The small population sizes and heterogeneous distribution of these rare fishes often complicate management and conservation efforts. Environmental DNA (eDNA) methods have the potential to improve detection of rare species but have only been incorporated into routine sampling methods to a limited extent by monitoring agencies. We conducted a study to evaluate the efficacy of eDNA for routine monitoring of larval smelt at Clifton Court Forebay, a State Water Project water export area within the SF Bay-Delta region. Enhancing the accuracy of data related to larval smelt abundance in this area will improve our understanding of potential impacts from State Water Project activities. Our study goals were to 1) test the capability of eDNA sampling methods to detect varying levels of biomass (n = 0, 1, 3, 10, 30, 60, 100) of larval Delta Smelt (< 20mm and < 40 dph), under ideal laboratory conditions, and 2) generate a standard dilution curve for larval Delta Smelt eDNA relative to varying levels of biomass. Our results confirm that eDNA can be used to detect Delta Smelt larvae across a range of biomasses (n = 1 to n = 100) under ideal conditions. We also found that eDNA signal strength increases somewhat linearly with biomass. Lastly, we successfully generated a standard curve to inform our statistical models for understanding detection probabilities under field conditions. These results have important implications for future eDNA monitoring and conservation efforts for smelt species and will inform future field-based experiments planned by DWR.

Authors

• Sarah Stinson*⁺, DWR, Sarah.Stinson@water.ca.gov
• Brian Schreier, DWR
• Gregg Schumer, Genidaqs
• Cheryl Dean, Genidaqs
• Daphne Gille, DWR

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Storm events are responsible for the transport of many pesticides into the aquatic environment. In California, late winter storms coincide with Delta Smelt spawn events thus placing their offspring at risk of exposure during sensitive developmental stages. Upon hatching embryos are at further risk, particularly of uptake of lipophilic compounds through their yolk-sac. We exposed yolk-sac Delta Smelt larvae to water samples associated with three rain events in March 2023, collected at four sites within the Delta: Ryer Island, Rio Vista, Ulatis Creek and the Toe Drain. After a 96-h exposure, we conducted behavioral studies using a DanioVision chamber, which were later analyzed using Ethovision tracking software. Targeted chemical analysis determined the presence of bifenthrin at concentrations previously shown to impact larval Delta Smelt behavior, at all sites for all three events. Other pesticides detected in the water included fipronil, fipronil sulfone, fipronil sulfide, and cyhalothrin. Exposure to all ambient samples resulted in significant hyperactivity. Furthermore, we observed changes in thigmotaxis (wall hugging), where the performance of exposed individuals displayed anti-anxiety-like (cross-well) behaviors. We will present this data, along with resulting alterations on larval velocity, freezing, cruising, and bursting, following exposure to Delta water samples. Our findings indicate that early larval exposure to commonly occurring pesticides may have detrimental effects on their behavior and development, potentially increasing their risk of predation.

Authors

• Andrea Chandler*⁺, School of Veterinary Medicine, UC Davis, andchandler@ucdavis.edu
• Cassandra Lievin, Unit of Environmental and Evolutionary Biology, University of Namur, and School of Veterinary Medicine, UC Davis
• R.E. Connon, School of Veterinary Medicine, UC Davis
• Mia Arkles, Southern Illinois University
• K.E. Huff Hartz, Southern Illinois University 
• M.J. Lydy, Southern Illinois University 
• A. Segarra, School of Veterinary Medicine, UC Davis

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

In the western regions of the United States, smelt species populations have significantly declined, necessitating their classification and protection under the Endangered Species Act. Specifically, the Delta smelt (Hypomesus transpacificus) is indigenous to the San Francisco Estuary (SFE), while the Longfin smelt (Spirinchus thaleichthys) inhabits the Northeast Pacific and adjacent river systems; both species are currently protected. Additionally, the Wakasagi (H. nipponensis) was introduced from Japan to California reservoirs in 1959. The morphological similarities among these species occasionally result in misidentification, thereby complicating conservation efforts. To address this issue, the present study employs geometric morphometric analysis to elucidate the morphological differences among these smelt species within SFE. The primary morphological distinction between Longfin smelt and Wakasagi lies in the curvature of the body section extending from the posterior end of the head to the dorsal region; it is convex in Longfin smelt and concave in Wakasagi. In contrast, Longfin smelt, and Delta smelt differ primarily in the anterior insertion points of the dorsal and pelvic regions, with Longfin smelt displaying a greater body depth than Delta smelt. The main difference between the body shape of Wakasagi and Delta smelt is noted in the anterior insertion points of the dorsal and anal regions, as well as in general body shape; specifically, Delta smelt exhibits a more slender and compact form compared to Wakasagi. These findings contribute to a more nuanced understanding of smelt morphology, thereby aiding in their accurate identification and subsequent conservation.

Authors

• Marzieh Asadi Aghbolaghi*, Department of Biological and Agricultural Engineering, University of California, Davis. masadi@ucdavis.edu
• Md Moshiur Rahman, 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

In recent decades, the distinct San Francisco population of Longfin Smelt (Spirinchus thaleichthys) has been in rapid decline, raising concerns regarding local extinction risk. Accurate age and growth data are needed, therefore, to inform population models and support the development of effective conservation strategies. At UC Davis, we are developing and testing methods to quantify annual age and growth of Longfin Smelt using seasonally produced transparent and opaque bands (“annuli”) in otoliths. Fish were selected from archived samples (from UC Davis and CDFW) based on numerous criteria including fork length, water year, and sampling location. Otoliths were then sectioned and polished in the transverse plane to expose annual increments for reconstructing age, growth, and life history information using image analysis and strontium isotope geochemical analysis (MC-LA-ICP-MS) to produce growth and life history chronologies for each individual. Thus far, we have generated age and growth estimates and geochemical profiles for more than 500 Longfin Smelt collected over the past 2 decades. Results will provide much-needed new information regarding variation in the age structure, growth rates, and life-histories for this imperiled native estuarine fish.

Authors

• Alex Lama*⁺, UC Davis awlama@ucdavis.edu
• Levi Lewis, UC Davis
• James Hobbs, CDFW
• Malte Willmes, Norwegian Inst. Nature Res.
• Nikolas Floros, UC Davis
• Alec Scott, UC Davis
• Sami Araya, UC Davis

* Presenting author
⁺ Early Career Award candidate

Abstract

The mortality that occurs to the fraction of an entrained fish population before fish are transported into the state (SWP) and federal (CVP) water projects is referred to as pre-screen loss (PL). Such mortality remains a critical unknown in the upper San Francisco Estuary (USFE). We conducted preliminary analyses on juvenile Longfin Smelt to: 1) examine their historical salvage patterns, 2) estimate their entrainment into SWP and CVP, and 3) estimate the proportion of fish lost to south Delta PL. Salvage and an index of salvage per potential spawner were computed for years 1993-2022. A preliminary abundance estimate for juvenile fish in the USFE was obtained using the California Department of fish and Wildlife 20-mm survey. Critical dry year 2022 was selected as a case study for objectives 2 and 3 as it was the peak salvage year since the pelagic organism decline. Entrainment loss into water projects was derived from previous surrogate mark-recapture studies conducted at the SWP and CVP. The PL in the south Delta was based on volume expansion of fish losses estimated within the SWP. Preliminary results showed: 1) salvage per potential spawner revealed the longest continuous period of higher than average entrainment losses for juvenile Longfin Smelt occurred during the record drought 2020-2022, 2) the estimated number of juvenile Longfin Smelt entrained into the south Delta water projects in year 2022 represented ca. 1−5% of the population, and 3) the projected percent of the Longfin Smelt population lost to south Delta PL in year 2022 varied widely and tended to greatly exceed entrainment losses at the water projects. These initial findings support the need for empirical quantification of PL in Longfin Smelt in dry and critically dry years to inform life-cycle models in this species.

Authors

• Gonzalo Castillo*, U.S. Fish & Wildlife Service, Gonzalo_Castillo@fws.gov
• Walter Griffiths, California Department of Fish & Wildlife

* Presenting author

No poster image available.

Abstract

Long-term persistence of the endangered Delta Smelt (Hypomesus transpacificus) will depend, in part, on whether the species harbors the genetic variation necessary to adapt to changing environmental conditions such as warm temperatures. Temperatures in the San Francisco Bay-Delta are increasing and extreme temperature spikes are becoming more common. The availability of additive genetic variation for traits that affect fitness directly determines the ability to evolve; however, nothing is currently known about the presence of genetic variation for resistance to elevated temperature in Delta Smelt. We performed a quantitative genetics experiment to test whether Delta Smelt harbor the necessary genetic variation for adaptation to elevated temperatures. We established crosses between wild and hatchery-reared (domesticated) fish and raised siblings from each family in both an optimal temperature (15 ℃) and an elevated temperature (18 ℃). We estimated thermal tolerance (Critical Thermal Maximum; CTM) of 3,000 fish raised in these two thermal environments. Our experiments show that fish reared at warmer temperatures had higher CTMs and fish that had longer ancestry in the hatchery also had higher CTMs. We genotyped 3000 fish and identified SNPs important for thermal tolerance using GWAS. Together, this information can be used to manage the refuge population and inform supplementation by maintaining ecological genetic variation that may be crucial for resilience in a warming Delta.

Authors

• Joanna Griffiths*⁺, University of California, Davis jsgriffiths@ucdavis.edu
• Moshiur Rahman, FCCL
• Amanda Finger, UC Davis
• Brittany Davis, DWR
• Tien-Chieh Hung, FCCL
• Nann Fangue, UC Davis
• Andrew Whitehead, UC Davis

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

The Spring Kodiak Trawl (SKT) was designed to improve the detection rate of adult Delta Smelt (Hypomesus transpacificus) during their spawning season in the San Francisco Estuary. This survey was initiated in 2002 following the conclusion of the Spring Midwater Trawl in 2001 because of its improved efficiency in catching adult Delta Smelt. The primary goal of the SKT is to provide valuable information about the population dynamics, reproductive success, and habitat use of Delta Smelt. The SKT employs surface trawls to sample the top 1.8 meters of the water column. It covers a total of 40 sampling stations distributed throughout the San Francisco Estuary, including a station in the Napa River, and extending up the Sacramento and San Joaquin Rivers. These stations are sampled once per month from January to May, which corresponds to the Delta Smelt spawning season. This study performed dissections in the field to determine the proportions of unripe, ripe, and spent Delta Smelt throughout the spawning season. Providing near-real time gonadal maturity data to water managers was used to reduce adult entrainment and infer whether the next generation might have hatched near water export pumps. The Spring Kodiak Trawl survey recently concluded in 2023. This poster provides a project overview and summary of survey results over the 22-year study.

Authors

• Jennifer Oceguera Zavala*⁺, California Department of Fish and Wildlife jennifer.oceguerazavala@wildlife.ca.gov
• Vanessa Mora, CDFW
• Jessica A. Jimenez, CDFW

* Presenting author
⁺ Early Career Award candidate

Abstract

The reproduction success of fish is directly related to sperm motility, which can be influenced by several factors, including the duration between sperm activation intervals. This study provides findings that can contribute to conservation and management efforts by examining the impact of distinct activation time intervals on sperm motility in endangered delta smelt (Hypomesus transpacificus), threatened longfin smelt (Spirinchus thaleichthys), and introduced wakasagi (H. nipponensis). Using a systematic experimental design, sperm samples were activated with freshwater and evaluated across various activation time intervals (0-5, 20-25, 30-35, 60-65, 120-125, 180-185, 240-245, and 300-305 sec) and then analyzed for sperm motility traits using OpenCASA software. The study also evaluated the influence of male fork length on sperm traits. The analysis revealed that the immediate activation window (0-5 sec) showed significantly high sperm motility across species boundaries, underscoring the crucial role of rapid sperm activation in boosting motility and potentially enhancing reproductive success. This study provides critical insights into the temporal dynamics of sperm motility across three fish species with different conservation statuses. The pronounced effect of activation time on sperm motility, regardless of species, along with the significant influence of male size on sperm traits, underscores the necessity for a comprehensive understanding of reproductive biology in conservation and management strategies. The findings offer a substantial foundation for further research in fertility dynamics, potentially aiding the formulation of informed conservation policies for endangered and threatened species.

Authors

• Md. Moshiur Rahman*, Fish Conservation and Culture Laboratory, Department of Biological and Agricultural Engineering, University of California Davis, momrahman@ucdavis.edu
• Tien-Chieh Hung, Fish Conservation and Culture Laboratory, Department of Biological and Agricultural Engineering, University of California Davis

* Presenting author

No poster image available.

Abstract

Thiamine (vitamin B1) deficiency complex (TDC) was first observed in juvenile California Chinook salmon in early 2020 after changing ocean conditions altered the marine food web. Females low in this essential vitamin returning to freshwater to spawn were unable to allocate sufficient thiamine to their eggs needed for healthy development of their progeny. This led to high mortality rates observed in juveniles at hatcheries along with signs of TDC such as sporadic swimming patterns. A multi-agency collaboration was launched to investigate the widespread nature of this nutritional deficiency among California salmonids, as well as understand its causes and impacts. Egg surveillance since 2020 has revealed an increasing prevalence of TDC in nearly all Central Valley populations of Chinook salmon and steelhead. Lower levels of thiamine have been linked to salmon diets dominated by the booming population of northern anchovies off California coasts. High activity of thiaminase, a thiamine-degrading enzyme, has been found in these anchovies, a contributing factor to TDC emergence in many species. Tissue samples from adult Chinook salmon females reveal a shift in diet diversity since TDC emergence. Laboratory studies were conducted to develop the relationship between egg thiamine concentration and survival of progeny. This relationship was applied to egg surveillance measurements to estimate population-level impacts of thiamine-dependent mortalities. Disruption to ocean food webs has been implicated in the poor nutrition of California salmon and TDC has emerged as a new stressor impacting already threatened salmon populations.

Authors

• Abigail Ward*⁺, UC Davis Center for Watershed Sciences, abbward@ucdavis.edu
• Rachel Johnson, NOAA/ NMFS Southwest Fisheries Science Center
• Carson Jeffres, UC Davis Center for Watershed Sciences 
• Nate Mantua, NOAA/ NMFS Southwest Fisheries Science Center
• Jacques Rinchard, State University of New York, Brockport
• Steve Litvin, Monterey Bay Aquarium Research Institute
• Steve Lindley, NOAA/ NMFS Southwest Fisheries Science Center
• Thomas Williams, NOAA/ NMFS Southwest Fisheries Science Center
• Anne Todgham, UC Davis
• Miles Daniels, NOAA/ NMFS Southwest Fisheries Science Center
• Dale Honeyfield, United State Geological Survey, retired
• Taylor Lipscomb, U.S. Fish and Wildlife Service
• Kevin Kwak, California Department of Fish and Wildlife
• John Field, NOAA/ NMFS Southwest Fisheries Science Center
• Bruce Finney, Idaho State University

* Presenting author
⁺ Early Career Award candidate

No poster image available.

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. Water quality data collected during the 2019, 2022, and 2023 NDFS studies will be used due to the varying amounts of precipitation and controlled flow efforts during those years. This will be compared to catch data from the Enhanced Delta Smelt Monitoring (EDSM) program taken from areas between Lisbon Weir and Suisun Bay during the months of potential flow actions in an effort to compare food availability and fish abundance. Food availability will be based on chlorophyll-a and other nutrients, which are an indicative of phytoplankton biomass. We will assess the catch per unit effort (CPUE) of planktivorous fishes, specifically Mississippi Silversides, juvenile American Shad, and Osmeridae species using EDSM catch data. This comparison can give insight to how various flow actions can affect nutrient levels and fish populations in the delta.

Authors

• Eric Louwerens*⁺, US Fish and Wildlife Service, eric_louwerens@fws.gov
• Alex Haner, US Fish and Wildlife Service
• Paula Higginson, US Fish and Wildlife Service
• Mentor: Erik Huber, US Fish and Wildlife Service

* Presenting author
⁺ Early Career Award candidate

Abstract

Long-term declines in threatened and endangered fish species in SFE may be, in part, due to lack of food resources during critical life stages. Two important prey species for young fish, the calanoid copepods Pseudodiaptomus forbesi and Eurytemora carolleeae, alternate in abundance in a consistent seasonal cycle. What drives the persistence of these patterns? We are investigating the mechanisms behind these seasonal patterns during key transition periods – spring (E. carolleeae begins to decline), spring-summer (P. forbesi abundance levels off), and autumn (P. forbesi begins to decline). We collected copepods from the field to estimate copepod abundance and egg production rates, and to set up lab-based growth rate experiments. During growth rate experiments, copepods were incubated in ambient water (containing ambient prey) or ambient water supplemented with a ≥ 10 µg chl L-1 mixture of 4-5 phytoplankton species of various sizes, morphologies and motilities. During the seasonal peaks of both copepods, food supplements provided little or no boost to copepod growth rate, but a larger (albeit still modest) boost was observed as each species approached the time of its seasonal decline. Our results so far support the theory that, in our study sites, Pseudodiaptomus forbesi growth and reproductive rates during the autumn seem to be limited by food resources, and this likely contributes to the declining population during the autumn transition. This trend was similar for Eurytemora carolleeae in spring, although the underlying mechanism may not be identical to that for P. forbesi. A better understanding of the seasonal pattern of food (zooplankton) available for smelt in the upper San Francisco Estuary will show the times of the year when proposed management actions in SFE, intended to bolster food supply (i.e., phytoplankton for zooplankton), will most effectively fill gaps in food availability for fish species of concern.

Authors

• Anne Slaughter*, Estuary & Ocean Sciences Center, SFSU, aslaught@sfsu.edu 
• Toni Ignoffo, Estuary & Ocean Sciences Center, SFSU
• Michelle Jungbluth, Estuary & Ocean Sciences Center, SFSU
• Wim Kimmerer, Estuary & Ocean Sciences Center, SFSU

* Presenting author

No poster image available.

Abstract

Strategic releases of water through Yolo By-Pass in summer and fall (collectively referred to as “North Delta Food Subsidy actions”) are intended to ameliorate downstream food limitation for Delta Smelt (Hypomesus transpacificus) and other pelagic fish species. Augmentation of flows in the Toe Drain during these months can increase local productivity, but there is substantial uncertainty regarding the spatial and temporal sphere of influence on consumers. To understand the mechanisms that result in increased productivity and document the spatiotemporal impacts of these management actions on fish, we assessed the potential for using stable isotope tools to quantify food web dynamics associated with flow releases. Representative ecosystem constituents (particulate organic matter, macrophytes, zooplankton, macroinvertebrates, and fish) were collected from six locations ranging from high upstream in the Toe Drain to the Rio Vista Bridge downstream and analyzed for isotopes of carbon (δ13C), nitrogen (δ15N), and sulfur (δ34S). Preliminary results indicated spatial patterns in all three isotopes for particulate organic matter, zooplankton, and macroinvertebrates, indicating strong potential for use of stable isotope tools to track the impact of flow actions on local food webs.

Authors

• Danielle Palm*⁺, U.S. Geological Survey, dpalm@usgs.gov
• Marissa Wulff, U.S. Geological Survey
• Matt Young, U.S. Geological Survey
• Eric Holmes, California Department of Water Resources
• Christina Lupoli, California Department of Fish and Wildlife
• Kristi Arend, Bureau of Reclamation
• Laura Twardochleb, California State Water Resources Control Board
• Brittany Davis, California Department of Water Resources

* Presenting author
⁺ Early Career Award candidate

Abstract

The Cache Slough Complex (CSC) is an important component of the California Delta which provides critical habitat for aquatic species, including Delta Smelt, flood protection for nearby cities, and water delivery for agricultural and municipal uses. Once a productive ecosystem supporting robust native fish populations, the CSC faces issues of reduced geomorphic complexity, non-native species competition, water diversions, and a warming climate, all of which has impacted the food web causing challenges for native species. Despite these alterations and stressors, the CSC represents one of the largest tidal wetland habitats in the Delta and contains habitat which has been deemed critical for the persistence of Delta Smelt. The North Delta Food Subsidies (NDFS) project was conceived to improve habitat in the CSC by creating managed flow pulses through the Yolo Bypass Toe Drain into the CSC. Multiple summer/fall flow pulses over the past decade have been implemented in coordination with local landowners. Nutrient concentrations have been monitored as well as phytoplankton and zooplankton responses before, during and after management actions. Despite some initially promising results, uncertainty about the efficacy of management actions in subsequent years has led to continued assessment of flow actions and other factors that potentially affect habitat quality in the region. With no managed flow pulse conducted in the summer/fall of 2023, this was an opportunity to investigate differences in lower trophic seasonal and regional patterns with other comparable wet years with managed flow actions (2019) and without managed flow actions (2017 & 2023). In these wet years, we expect to find a seasonal pattern as the ecosystem transitioned from a productive spring following extensive flooding with possible influences from other point sources such as regional wastewater effluents or nearby agriculture.

Authors

• Alexandria Evans*⁺, California Department of Water Resources, alexandria.evans@water.ca.gov
• Alexa Camilleri Evans*⁺, California Department of Water Resources
• Luke Olson, California Department of Water Resources
• Mackenzie Miner, California Department of Water Resources
• Eric Holmes, California Department of Water Resources
• Brittany Davis, California Department of Water Resources

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

The experimental North Delta Food Subsidies Study is an adaptive management strategy of the Delta Smelt Summer-Fall Habitat Action. It is designed to improve understanding of the processes by which the Yolo Bypass may provide a summer-fall food web subsidy for Delta Smelt in the Cache Slough Complex and downstream, especially with augmented summer flows, such as the experimental managed flow action conducted in 2016. The baseline conditions without managed actions are key to interpretation of the actions’ food web effects. Here we describe data collected from 2017 to 2023 over a spectrum of hydrologic conditions including years with and without experimental, managed flow actions. Water quality, nutrient conditions, chlorophyll, and primary production were measured along a downstream transect from Ridge Cut Slough near Knights Landing through the Yolo Bypass to the Sacramento River at Rio Vista with seven stations sampled consistently over the years, up to six times each summer-fall. Consistent spatial patterns emerged, with clear distinctions in many parameters between upstream locations in the Yolo Bypass Toe Drain and downstream in the Cache Slough Complex (Liberty Island to Rio Vista). Upstream sites were characterized by high turbidity, high nitrate (up to 200 uM) and phosphate (> 40 uM), high phytoplankton biomass (chlorophyll often peaking above 40 ug/L). Downstream, water was less turbid and ammonium higher due to the influence of the Sacramento River, until summer 2021 following the Regional San wastewater treatment plant upgrade. In 2022, nitrate and chlorophyll were much lower than other years at upstream sites, possibly a result of historically lower fields farmed, irrigated, and fertilized (~1% of normal rice planting) due to the extreme drought conditions. Forthcoming results aim to demonstrate how these different sources of nutrients fuel elevated productivity and food subsidies, knowledge that is needed to evaluate future management actions.

Authors

• Frances Wilkerson*, EOS Center, San Francisco State University, fwilkers@sfsu.edu
• Sarah Blaser, EOS Center, SFSU
• Reed Hoshovsky, EOS Center, SFSU
• Ben Gustafson, EOS Center, SFSU
• Laura Twardochleb, California State Water Resources Control Board
• Jared Frantzich, CA Department of Water Resources
• Mackenzie Miner, CA Department of Water Resources
• Brittany Davis, CA Department of Water Resources
• Eric Holmes, CA Department of Water Resources
• Elena Huynh, CA Department of Water Resources

* Presenting author

No poster image available.

Abstract

The Sacramento-San Joaquin Delta is a vast river system that supports a diverse range of non-native and native fish species. It also serves as a major highway for juvenile salmonids migrating to the ocean. Increased predation from both native and non-native fishes along highly utilized juvenile travel routes is one of the first hurdles they must face when making their journey to the ocean. Our goal for this poster is to use data from the Lodi Fish and Wildlife Office’s delta boat electrofishing survey, collected from 2018-2022, to identify potential seasonal distribution changes in piscivorous fishes and identify possible “hotspots” of predation that could affect juvenile salmonids traveling through the delta. We believe that there will be seasonal hotspots in piscivorous activity in areas highly utilized by juvenile salmonids. We also plan to examine salmon catch data from the Delta Juvenile Fish Monitoring program’s trawl and beach seine projects collected during the same time frame, to highlight possible areas of increased interaction. We are currently in the process of completing our results.

Authors

• Britany Perry*⁺, U.S. Fish and Wildlife Service, britany_perry@fws.gov
• Garret Smith*⁺, U.S. Fish and Wildlife Service
• Jacob Stagg, U.S. Fish and Wildlife Service

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

To gain a deeper understanding of long-term trends in aquatic food webs within the Bay-Delta region, accurate tracking of shifts in zooplankton species composition is crucial. We aim to advance non-invasive zooplankton sampling techniques by utilizing environmental DNA (eDNA) sampling. Using a process called 'metabarcoding,' we can identify species within a mixed community of organisms through Next-generation Sequencing. Each species’ unique genetic code allows for precise identification of organisms within the community. In this study, our metabarcoding tool specifically targets copepoda, amphipoda, and cladocera species to assess shifts in species composition and periodicity in zooplankton populations, which serve as essential food sources for larval and juvenile fish, including Delta and Longfin smelt.

Authors

• Allen Huynh*⁺, Genidaqs, allen.huynh@fishsciences.net
• Cheryl Dean, Genidaqs
• Jasmine Williamshen, Cramer Fish Sciences

* Presenting author
⁺ Early Career Award candidate

Abstract

Zooplankton monitoring in the San Francisco Estuary by IEP has produced an extremely valuable historical record of the food available to fishes. To assess the quantity of this food we need estimates of biomass for the zooplankton taxa present throughout the estuary. The goal of this project is to present the scientific community a well-designed, tested, and accurate set of tools for estimating biomass of zooplankton that can be applied to monitoring. Our approach was to calibrate zooplankton volume-to-carbon estimates from image analysis. Results showed that 2% glutaraldehyde was the best preservative to conserve fluctuations in volume and carbon content.

We sampled zooplankton taxa across various salinities to capture as many species as possible throughout the northern estuary, sorted the sample by taxon, measured, imaged, and analyzed each species on an elemental analyzer for carbon content. We have developed volume-to-carbon conversions for copepods (Eurytemora carolleaee, Pseudodiaptomus spp., Acanthocyclops sp., Acartiella sinensis, Acartia sp., Sinocalanus doerrii, and Tortanus dextrilobatus), cladocerans (Daphnia magna, Bosmina sp., and Diaphanosoma sp.) and mysids (Neomysis kadiakensis, Hypercanthomysis longistrostis). We will continue to calculate relationships for more taxa and work to develop a technique to estimate carbon from bulk samples to streamline our approach and provide the scientific community a reliable and economical approach to estimating food quantity for fishes.

Authors

• Toni Ignoffo*, SFSU, tignoffo@sfsu.edu
• Anne Slaughter, SFSU
• Michelle Jungbluth, SFSU
• Wim Kimmerer, SFSU

* Presenting author

No poster image available.

Abstract

Fish monitoring programs in the delta provide valuable information about the ecosystem, but some sampling methods are not the best for detecting species associated with cover such as Warmouth (Lepomis gulosus). However, the Lodi Fish and Wildlife Office’s (LFWO) boat electrofishing survey can provide insight into these species because electrofishing can sample in obstructed habitats unlike net-based surveys like trawling or seining.

We are planning to use data from boat electrofishing to explore the distribution and specific habitat preferences of a non-native centrarchid associated with vegetative cover, the Warmouth, within the Sacramento-San Joaquin delta. We aim to gain insight into the Warmouth’s spatial distribution and density as a function of sample location and catch per unit effort in fish per minute. We will also look at detection probability within different habitat types. Finally, we plan to look at potential environmental influences (temperature, dissolved oxygen, turbidity) and fish assemblage associations that might predict Warmouth presence.

Authors

• Olivia Bertelsen, US Fish and Wildlife Service
• Jacob Stagg*, US Fish and Wildlife Service, jacob_stagg@fws.gov

* Presenting author

Abstract

The Delta Stewardship Council hosted the 1st Science for Communities Workshop (SFC 1.0) in October of 2022. The goal of this event was to help address social and environmental issues community members face within the Delta and surrounding areas by fostering relationships between community-based organizations (CBOs) with academic and agency scientists. The event accomplished this by bringing together six CBOs (California Indian Environmental Alliance, Little Manila Rising, Public Health Advocates, Restore the Delta, Sacramento Regional Coalition to End Homelessness, and Sustain our Abilities) and 32 scientists from state agencies or universities, and the community. During the event, CBOs were able to share environmental justice related research topics that they would like to explore within the Delta region. CBO representatives also shared resources to help address these issues and presented the results of their collaboration. CBOs and scientists were paired based on research topic interest and scientist expertise to undertake joint research projects. Four out of the six CBOs selected research interests that directly relate to water quality and contamination in the Delta. Other research interests included addressing how negative environmental impacts affect public health and socioeconomic status in disadvantaged communities and how climate change will impact people with disabilities within the Delta. In a post-event survey, 77% of the surveyed attendants said they would attend again and 63% cited their primary motive in attending was to network with members of the community. Feedback from the CBOs following the event is that they would like to see more participation from marginalized and younger members of local communities in addition to more networking opportunities. This poster will outline the research topics the CBOs shared during SFC 1.0 and have selected in anticipation of the SFC 2.0 event, evaluation material and community feedback from the SFC 1.0, and trajectories for improving SFC 2.0.

Authors

• Hannah Chaney*, Delta Stewardship Council, Hannah.Chaney@deltacouncil.ca.gov
• Megan Thomson*, Delta Stewardship Council, Megan.Thomson@deltacouncil.ca.gov
• Martina Koller, Delta Stewardship Council
• sciforcommunities@deltacouncil.ca.gov

* Presenting author

No poster image available.

Abstract

To effectively manage species and habitats at multiple scales, population and land managers require rapid information on wildlife use of managed areas and responses to landscape conditions and management actions. GPS tracking studies of wildlife are particularly informative to species ecology, habitat use, and conservation. Combining GPS data with administrative data and a diverse suite of remotely sensed, geo-referenced environmental (e.g., climatic) data, would more comprehensively inform how animals interact with and utilize habitats and ecosystems and our goal was to create a conceptual model for a system that would accomplish this – the ‘Automated Interactive Monitoring System (AIMS) for Wildlife’. Our objective for this study was to build a “proof of concept” system based on our 8-year GPS tracking dataset of ~11 million locations from 1338 individual (16 species) avifauna and make actionable, real-time data on animal movements and trends available to managers and stakeholders for rapid application in day-to-day management. The AIMS ecosystem consists of three primary components: 1) data ingestion 2) data processing and storage and 3) product delivery. Outputs can be easily customized into customized wildlife reports (CWR’S), web applications, wildlife alerts and basic data summaries emphasizing the broad application of an animal movement data source. Utilizing diverse, extensive telemetry data streams through scientific collaboration can aid managers and conservation stakeholders with short and long-term research and conservation planning and help address a cadre of issues from local-scale habitat management to improving the understanding of landscape level impacts like drought, wildfire, and climate change on wildlife populations.

Authors

• Michael Casazza*, USGS Western Ecological Research Center, mike_casazza@usgs.gov
• Austen Lorenz, USGS Western Ecological Research Center
• Cory Overton, USGS Western Ecological Research Center
• Elliott Matchett, USGS Western Ecological Research Center
• Andrea Mott, USGS Western Ecological Research Center
• Desmond Mackell, USGS Western Ecological Research Center
• Fiona McDuie, San Jose State University Research Foundation, Moss Landing Marine Laboratories

* Presenting author

Abstract

Examining fish passage success through a designed facility in the Fremont Weir following recent flooding and weir overtopping events. Collaborative efforts between state and federal agencies, landowners, and county supervisors allowed operation of the facility outside permitted timelines and resulted in successful fish passage for threatened or endangered species that would have otherwise been stranded. Key topics: Fish passage facility, designed floodplain inundation, threatened or endangered species, science communication, reduced migratory delays, floodplain restoration.

Authors

• Jeff Jenkins*, CA Dept of Water Resources, jeff.jenkins@water.ca.gov

* Presenting author

No poster image available.

Abstract

AIMS for Wildlife is a system specifically designed facilitate more effective wildlife management by simplifying the interpretation of complex wildlife GPS telemetry data. Specifically, AIMS generates highly reproducible Customized Wildlife Reports that include refuge, state, species, and joint venture reports; all of which can be tailored by date, species, and location. Through a user-centric approach designed in close collaboration with wildlife biologist and decisionmakers, these reports are presented in interactive easy-to-understand tables, maps, figures, and formats. This feature makes them accessible to a broad range of users, ensuring that the tool meets the needs of those directly involved in wildlife management.

Customized Wildlife Reports are designed to improve access to wildlife GPS telemetry data and enhance its comprehensibility. The tool reduces the need for specialized skills such as GPS, data management, and GIS analysis. By transforming complex telemetry data into a more accessible resource at management-relevant spatial and temporal scales, Customized Wildlife Reports enhance the capacity of wildlife managers and stakeholders to make informed decisions and contribute to more effective conservation.

Authors

• Austen Lorenz*, USGS Western Ecological Research Center, aalorenz@usgs.gov
• Cory Overton, USGS Western Ecological Research Center
• Elliott Matchett, USGS Western Ecological Research Center
• Andrea Mott, USGS Western Ecological Research Center
• Desmond Mackell, USGS Western Ecological Research Center
• Fiona McDuie, San Jose State University Research Foundation, Moss Landing Marine Laboratories
• Michael Casazza, USGS Western Ecological Research Center

* Presenting author

No poster image available.

Abstract

The Sacramento-San Joaquin Delta, a critical and complex ecosystem, hosts a multitude of scientific endeavors conducted by diverse entities, including government agencies, academic institutions, non-governmental organizations, and private research groups. Despite concerted coordination efforts, a standardized inventory to track these activities has been notably absent. This deficiency hinders accountability and impedes opportunities for collaboration and coordination. Addressing this gap, the Delta Science Tracker emerges as a pioneering web-based platform, generously supported and spearheaded by the Delta Science Program. This publicly accessible hub is designed to centralize comprehensive information about science activities across the Delta landscape, providing an invaluable resource for researchers, managers, decision-makers, and the public alike.

The Delta Science Tracker's primary objective is to improve communication and connectivity within the Delta science community. In a landscape where the breadth and diversity of scientific work can be overwhelming, this platform offers a structured, easily navigable interface, enabling stakeholders to discern and engage with relevant projects and expertise.

In line with the Delta Science Plan's visionary concept of 'One Delta, One Science,' the Delta Science Tracker embodies a shared commitment to building a collective body of scientific knowledge. This dynamic resource has the capacity to adapt and inform future water and environmental decisions, thereby ensuring the long-term sustainability and resilience of the Sacramento-San Joaquin Delta.

Furthermore, in an era marked by escalating uncertainty regarding climate, water supply, and the Delta's native ecosystem, the imperative for multi-institutional collaboration has never been more apparent. The Delta Science Tracker serves as a catalyst for enhanced collaboration by connecting managers, policymakers, and scientists across disciplines and geographies. This collaborative approach is vital for making informed decisions that will shape the future of the Delta ecosystem and water resource management.

Authors

• George Isaac*, Delta Science Program - Delta Stewardship Council George.Isaac@deltacouncil.ca.gov
• The Science Tracker team at the Delta Science Program

* Presenting author

No poster image available.

Abstract

The Delta is the most significant water hub in California, providing essential water supply to communities, farms, and industries inside and outside the Delta. The Interagency Ecology Program Science Priorities for 2020-2024 focuses on Bay-Delta Resilience to climate change, where variables like salinity intrusion are identified as a major challenge for managing species of concern. During extended drought conditions, reduced freshwater inflows to the Delta make it more difficult to maintain the salinity levels needed to maintain beneficial uses for humans, fish, and wildlife in the Delta. Starting in 2022, the Delta Stewardship Council launched a series of workshops that engaged a wide range of interested parties to identify challenges associated with ocean salt intrusion in the Delta, identify knowledge gaps that must be filled to address those challenges, and lay the groundwork for a long-term collaborative adaptive management approach. This series included workshops, two funded independent research projects, and thematic focused working group meetings. One research project improves upon and demonstrates the use of high resolution hydrodynamic and salinity transport models in combination with the CalSim statewide water operations model to estimate potential water costs and savings associated with changes in Delta geometry and operations. The other research project explores the human dimensions of salinity management through interviews. The final workshop in early 2024 will synthesize results from these efforts and foster discussion about tradeoffs and next steps for a long term approach to adaptively managing salinity in the Delta.

This presentation will include preliminary results from the workshop series and the two research projects with an emphasis on lessons learned for adaptive management.

Authors

• Stephen Elser*⁺, Delta Stewardship Council, stephen.elser@deltacouncil.ca.gov
• Laurel Larsen, Delta Stewardship Council
• Dylan Chapple, Delta Stewardship Council
• Xoco Shinbrot, Delta Stewardship Council
• Christina Greene, University of Arizona
• Eli Ateljevich, California Department of Water Resources
• John DeGeorge, Resource Management Associates

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Drainage of land in the Sacramento-San Joaquin Delta has caused extensive oxidation of peat soils, lowering approximately 386 mi2 of land from 10 ft to as much as 29 ft below sea level. Although decades of subsidence have already depleted peat soils in areas of the Delta, subsided lands continue to cause significant challenges, such as increasing costs to drain soils, declining arability for agricultural production, water quality degradation, vulnerability to levee failure and flooding, and substantial emissions of greenhouse gases in areas where drained peat soils remain. A broad cross section of stakeholders, including public agencies and private sector parties, are developing and testing many different approaches to manage subsided lands. The scale of subsidence in the Delta and the severity of its consequences for Delta agriculture, greenhouse gas emissions, and water quality indicates a need to assess existing management of subsided lands and the social, cultural, and economic trade-offs among different management approaches. To help address this, the Delta Independent Science Board is working to synthesize and evaluate the state of science related to adaptive management of subsided lands and provide recommendations to address knowledge gaps. This poster will share emerging insights into scientific knowledge gaps, economic and decision-making perspectives from landowners and public agencies, as well as recommendations to improve the adaptive management of a complex Delta.

Authors

• Delta Independent Science Board, Edmund Yu*, edmund.yu@deltacouncil.ca.gov

* Presenting author

Abstract

The Yolo Bypass Salmonid Habitat Restoration and Fish Passage Project (Big Notch Project) is a nearly complete environmental infrastructure facility located in the Fremont Weir that aims to help restore California’s native salmonid and sturgeon populations. This project is jointly funded by the California Department of Water Resources and the US Bureau of Reclamation to mitigate for the State Water Project and Central Valley Project. The Big Notch Project is likely to be operational by November 2024. The objectives of the Big Notch Project are to: 1. Create floodplain rearing habitat and entrain juvenile salmonids; 2. Reduce migratory delays and loss of adult anadromous fishes; and 3. Limit unforeseen impacts to existing land uses. The DWR Restoration Ecology Unit along with the multi-agency and multi-disciplinary Fisheries and Engineering Technical Team (FETT) have jointly drafted a protocol for responding with adaptive management if the project is not meeting one or more objectives. The team will use a variety of monitoring categories, including telemetry, sonar imagery, fish rescue data, rotary screw trap data, hydraulics, and land use impacts to inform the adaptive management process. This poster describes the monitoring and adaptive management process, explores the monitoring categories planned for this effort, and gives examples of potential adaptive management responses if intervention thresholds are exceeded.

Authors

• Brandy Smith*⁺, California Department of Water Resources, Brandy.Smith@water.ca.gov
• Hailey Mico, California Department of Water Resources, hailey.mico@water.ca.gov

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

The Black Sea jellyfish (Maeotias marginata) is a small hydromedusa that was introduced into the San Francisco Estuary in the 1950’s. Previous research conducted on this invasive species suggests that salinity and water temperature may affect distribution and abundance. We plan to explore catch data collected by the Enhanced Delta Smelt Monitoring (EDSM) Program to determine how abundance, distribution, and timing of blooms may vary over time as it relates to environmental factors (turbidity, conductivity, temperature, and dissolved oxygen). Our goal is to create a density map of these jellyfish blooms from year to year to gain insight on how these animals respond to extreme environmental events as this dataset covers several drought and flood years. This information may be useful in determining how changes in water and salinity levels caused by extreme weather events may alter the timing and density of blooms and how this may affect native species in the San Francisco Estuary.

Authors

• Jessica Falcon*⁺, U.S. Fish and Wildlife Service, jessica_falcon@fws.gov
• Jacob Stagg, U.S. Fish and Wildlife Service

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

A stable isotope of carbon (13C), when incorporated into bicarbonate, can be a powerful analytical tool to trace and quantify the uptake of inorganic carbon by phytoplankton. The fixation of bicarbonate occurs during photosynthesis and can be used as a proxy to determine phytoplankton productivity in aquatic systems. Phytoplankton productivity in the northern San Francisco Estuary (nSFE) is characteristically low, even among other comparable estuaries. Light limitation, a result of high turbidity, is a driving theory to explain low productivity. Counterintuitively, however, as water clarity in the nSFE increases, an expected rise in phytoplankton productivity has not been observed. A similar counterintuitive observation occurs when comparing the turbid Yolo Bypass floodplain (YB) where productivity is high and the relatively clear Sacramento River where productivity is low. A parallel theory to light-limitation is that phytoplankton in these systems are chronically low-light adapted, hindering productivity when conditions are ephemerally optimal. We present over 70 ‘productivity versus irradiance’ curves along a transect of the YB (5 stations) and nSFE (4 stations) downstream from West Sacramento to Grizzly Bay between March and November of 2023. The initial slopes of these curves indicate the efficiency at which phytoplankton utilize light and the saturation point indicates the photosynthetic capacity of phytoplankton. Initial results show a downstream trend of increasing efficiency in light utilization by phytoplankton, with a variable downstream trend in photosynthetic capacity. This suggests that a physiological change is occurring in phytoplankton as they are advected downstream. Further processing and analysis of this data may illuminate where along this transect this physiological change is occurring and what factors may be the cause. These results can lead water managers to a more thorough understanding of hydrologic factors controlling the base of the food web.

Authors

• Reed Hoshovsky*⁺, SFSU EOS, rhoshovsky@sfsu.edu
• Frances Wilkerson, SFSU EOS
• Mackenzie Miner, CADWR

* Presenting author
⁺ Early Career Award candidate

Abstract

The invertebrate community within the San Francisco Bay Delta faces significant stressors, particularly from storm-driven contaminants including phenylpyrazole and pyrethroid insecticides. These stressors impacts the Bay-Delta food web through shifts in prey items and invertebrate community structures. There have been recorded instances of invertebrates evolving resistance to insecticides, particularly the non-target crustacean Hyalella azteca, which suggests ecological impairment and contributes to trophic transfer of high insecticide concentrations to fish. However, the extent of adaptive resistance across invertebrate communities is not known. To better understand the extent of adaptive resistance in the San Francisco Bay Delta, common invertebrates were collected for evaluation of resistance in two genes: resistance to dieldrin (RDL) and voltage-gated sodium channel (VGSC). These genes are common targets of phenylpyrazole and pyrethroid insecticides and mutations in these genes can confer resistance to these insecticides. The collected invertebrates were divided by their orders, including Trichoptera, Plecoptera, Diptera, Amphipoda, Cladocera, Copepoda, Ephemeroptera, and Odonata based on their taxonomic identification. For each order and gene, degenerate primers were made for RDL and VGSC and tested for their validity on a small number of samples from each order. In addition, cytochrome oxidase I (CO1) was used to identify organisms to genus or species level. To determine if invertebrates collected from different regions of the San Francisco Bay Delta have developed resistance to phenylpyrazole or pyrethroid insecticides, we are investigating target site mutations in RDL and VGSC. The prevalence of resistance varies across different orders with some aquatic insects showing no detection of developed resistance. In this poster, we will present our final results of the resistance analysis across different invertebrate species in the Delta and discuss the potential implications for fish species.

Authors

• Helen Poynton*, University of Massachusetts Boston helen.poynton@umb.edu
• Irina Polunina-Proulx, University of Massachusetts Boston
• Elijah Wallace, Franklin and Marshall College
• Taryn Broughal, University of Massachusetts Boston
• Spencer Caddigan, University of Massachusetts Boston
• Sharon Lawler, University of California Davis
• Richard Connon, University of California Davis
• Michael Lydy, Southern Illinois University

* Presenting author

No poster image available.

Abstract

Improving the existing ability to predict phytoplankton blooms in the San Francisco Estuary/Delta (SFE) is key to management actions designed to enhance food production for Delta Smelt and for evaluating the likelihood of HABs, such as the recent red tide in Central SFE. Phytoplankton blooms need a nutrient base to occur and in the SFE the major source is nitrate, the largest pool of DIN. However, the other form of DIN, ammonium may occur at levels that can repress the uptake and assimilation of nitrate by phytoplankton - a well know inhibitory role of ammonium in higher plant physiology. The sequence of bloom development in SFE results from this interaction. In Phase 1 ammonium is taken up by the phytoplankton, biomass increases, and the ammonium concentration drops below inhibitory levels; In Phase 2 ammonium and nitrate uptake together result in rapid increase in phytoplankton biomass, a bloom; finally in Phase 3 – nitrate is drawn down to zero and phytoplankton biomass decreases by sinking and grazing. An important, forgotten factor that also contributes to the bloom is the initial seed stock concentration of phytoplankton. The higher the initial biomass the more rapid the nitrate will be drawn down to zero and the bloom will be confined to a short period and a small area. Multi-dimensional plots of chlorophyll, ammonium and time-to- nitrate depletion provide a platform for analyzing bloom potential. Examples of using this platform will be shown from pre- and post- Echowater Regional San wastewater treatment plant upgrade conditions in the northern SFE, and also Central SFE during the Heterosigma red tide of 2022. Bloom prediction requires monitoring nitrate and ammonium and chlorophyll concentrations. Using these parameters that could be measured with in situ continuous analyzers offer a simple approach to meet IEP adaptive management concepts.

Authors

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

* Presenting author

Abstract

To develop a robust program for monitoring cyanobacterial harmful algal blooms (cyanoHABs), Solid Phase Adsorption Toxin Tracking (SPATT) samplers and collection of whole water cyanotoxin samples were added to pre-existing water-quality monitoring sites operated by the U.S. Geological Survey in the Delta. The goal of this research is to evaluate the utility of deploying SPATT samplers to monitor for cyanotoxins in estuaries, specifically how SPATT sampler data complement data from discrete whole water samples. From October 2020 through October 2022, SPATTs and whole water samples were collected every two to four weeks alongside water-quality samples at six sites spanning salinities of 0 to 8 PSU. Cyanotoxins were analyzed with liquid chromatography tandem mass spectrometry (LC-MS/MS). Of 204 SPATT samplers analyzed, five toxin classes were detected, with a total of 72 microcystin, 50 anabaenopeptin, 39 anatoxin, 18 cylindrospermopsin, and 11 nodularin detections. The highest concentrations were observed for microcystins (mean = 278, max = 3,621 ng/g), followed by anabaenopeptins (mean = 62.1, max = 915 ng/g). Out of 248 whole water samples, three classes of cyanotoxins were detected:  47 anabaenopeptin, 8 microcystin, and 4 anatoxin detections. Of the whole water samples, the highest concentrations were observed for anabaenopeptins (mean = 11.3, max = 219 µg/L), followed by anatoxins (mean = 3.70, max = 11.6 µg/L), and microcystins (mean = 0.118, max = 0.31 µg/L). Because there are multiple analytical methods for measuring cyanotoxins, twelve whole water samples were submitted for analysis by enzyme-linked immunosorbent assay (ELISA) for comparison with LC-MS/MS results. One microcystin detection analyzed via ELISA contained 1.81 μg/L microcystin, which exceeded the California tier 1 trigger threshold of 0.8 μg/L. Study results demonstrate the high sensitivity of SPATT samplers and their ability to detect cyanotoxins at low environmental concentrations.

Authors

• Katrina Cone*⁺, USGS, kcone@usgs.gov
• Angela Hansen, USGS
• Tamara Kraus, USGS
• Crystal Sturgeon, USGS
• Judy Westrick, Wayne State University
• Keith Bouma-Gregson, USGS

* Presenting author
⁺ Early Career Award candidate

Abstract

Location and time have major implications for habitat restoration outcomes, often dictating physical conditions, correlating with species abundance, influencing genetic variance, and forming the foundation for biodiversity. This study delves into fluctuations in environmental conditions and fish biodiversity within a designed tidal wetland, the Dutch Slough Tidal Marsh Restoration Project. The challenges presented by the intricacy of reticulated tidal habitats, which prove difficult to survey using traditional net methods, along with sensitive species “take” restrictions, necessitated the incorporation of low impact survey techniques: DNA metabarcoding and the Aquatic Species and Habitat Sampling Platform (Platform). A sampling design was implemented before and after the breaching of levees, thus allowing observation of environmental and fish community changes resulting from merging the restored habitat with the San Francisco Estuary.

Combining fish detection through eDNA and video sampling with associated physical data within this habitat provides insights into fish behavior, interactions, and habitat utilization. Together, these methodologies revealed that post-breach, fish biodiversity in the restored habitat surged, with fish from the surrounding area colonizing the newly accessible environment.

Data analysis for this project is ongoing, with a projected completion date of late 2023. Preliminary analysis of DNA data has revealed that non-native species were approximately double the number of native species, mirroring the inherent condition of the Estuary. Out of the 42 fish species identified through ongoing eDNA surveys, five protected native species, including Chinook Salmon, Green Sturgeon, Longfin Smelt, Pacific Lamprey, and Rainbow Trout, were discerned within the revitalized habitat. We hypothesize that fish video and physical data collected by the Platform will mirror the DNA data. By amalgamating DNA metabarcoding with video observation and environmental conditions, this joint research offers a comprehensive understanding of fish biodiversity and the dynamic interplay of species within restored habitats.

Authors

• Katie Karpenko*⁺, Cramer Fish Sciences, katie.karpenko@fishsciences.net
• Lis Cordner, Cramer Fish Sciences
• Scott Blankenship, Cramer Fish Sciences
• Cheryl Dean, Cramer Fish Sciences
• Randy Mager, DWR (retired)
• Molly Ferrell, DWR
• Joseph Merz, Cramer Fish Sciences

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

In 2023, the DWR Division of Regional Assistance drone team, consisting of an FAA-licensed UAV Operator/Pilot, a licensed land surveyor, a GPS assistant, and a visual observer will plan, coordinate, fly, and collect a series of high-resolution aerial images videos, and 3-dimensional digital data at Paradise Cut in the southern Sacramento-San Joaquin Delta. Paradise Cut typically acts as a backwater tidal Delta slough, but also consists of a rock weir that is intended to alleviate high flows (17,000 cfs) from the San Joaquin River, and act as a flood control system for the city of Stockton, CA. Due to the wet water year and extended high flows in the San Joaquin River in 2023, the drone team planned to capture imagery and video footage of the floodplain area within Paradise Cut and after the floodwaters receded. Two flights were conducted in Paradise Cut, 1) during June 6th to capture a flooded period and 2) on August 9th to capture normal to low flow period. The objective of the project is to generate survey grade photogrammetry to inform DWR’s efforts associated with Delta modeling, flood planning, long-term water quality monitoring studies, and public education. The drone team was able to achieve this objective by using the RTK Phantom drone which consists of high GPS accuracy and Trimble survey equipment, and installed ground control points to create survey grade photogrammetry. Finally, after all photogrammetry was collected for the two flights, the photos and GCPs were uploaded into ArcGis Pro to create a high quality orthomosaic of the entire Paradise Cut levee to levee channel area to visualize flow patterns and flooded landscapes. The use of drone technology in DWR environmental monitoring projects are proving to be invaluable, and data acquisition using drones continues to provide more accurate, efficient, and safer ways to collect georeferenced datasets.

Authors

• Katherine Cabras*⁺, DWR, NCRO, DRA, WQES, Katherine.cabras@water.ca.gov
• Jared Frantzich, Department of Water Resources

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Water quality is a critical component of water security. As climate change continues to challenge sustainable water resource management, there is an increasing need for near real-time water quality monitoring and early warning forecasts to inform water resource managers, ecosystem managers, and the public. AquaWatch is a collaboration between California and Australia that is seeking to develop a ‘weather service’ for water quality for California, Australia, and eventually, globally. AquaWatch is integrating ground-to-space based water quality monitoring with advanced, cloud-based data analytics forecasts within an Internet of Things (IoT) framework. The project seeks to use existing networks of in situ water quality sensors and contribute additional in situ sensors for high-accuracy ground-based measurements. These will be combined with satellite observations made from a constellation of existing and future custom-built earth observing satellites to scale highly precise water quality across large regions.

The first California pilot site is being deployed in the Sacramento-San Joaquin Delta, with a first focus on turbidity, followed by development for other optically active water quality constituents such as dissolved organic matter and algal blooms. The work is part of the Action Plan under the recently signed Memorandum of Understanding (MOU) between the Commonwealth of Australia and the Government of the State of California to address climate change and a transition to green energy. A critical facet of the MOU and the project is the exchange of scientific knowledge and technical expertise, and co-design of the system with local indigenous, public, and private water resource managers. The purpose of the poster presentation is to raise awareness of the project, seek input for the co-design process, and seek future opportunities for collaboration and exchange of knowledge and expertise.

Authors

• Erin Hestir*, University of California Merced, ehestir@ucmerced.edu
• Janet Anstee, Commonwealth Scientific & Industrial Research Organization (CSIRO), janet.anstee@csiro.au
• Dulcinea Avouris, U.S. Geological Survey, California Water Science Center, davouris@usgs.gov 
• Brian Bergamaschi, U.S. Geological Survey, California Water Science Center, bbergama@usgs.gov
• Tom Bergamaschi, U.S. Geological Survey, California Water Science Center, tbergamaschi@usgs.gov
• Darius Culvenor, Environmental Sensing Systems, darius.culvenor@sensingsystems.com.au
• Margaret Donoghue, Commonwealth Scientific & Industrial Research Organization (CSIRO), margaret.donoghue@csiro.au
• Alex Held, Commonwealth Scientific & Industrial Research Organization (CSIRO), alex.held@csiro.au
• Susan Ustin, University of California Davis, slustin@ucdavis.edu

* Presenting author

No poster image available.

Abstract

Drainage waters from managed agricultural lands can transport nutrients, particulate matter, carbon, and pesticides into receiving waterways. This transport of these constituents can significantly impact aquatic habitats, drinking water quality, and recreational uses. In the Sacramento-San Joaquin Delta, where much of the agricultural land has subsided below the level of surrounding waterways, water drainage via mechanical pumping is also crucial for the viability of agricultural activities and the protection of island infrastructure. Due to the high carbon content of Delta island soils, the regular and sustained discharge of drainage waters from islands to Delta waterways can also be a pathway for lateral loss of carbon and associated constituents, which can exacerbate ongoing land subsidence. Because many Delta islands are currently or planned to undergo land use and land cover (LULC) changes, such as wetland restoration and changing cropping patterns, with the goal of reversing land subsidence and reducing carbon emissions, constraining how LULC changes affect island chemical budgets is important to contextualizing the efficacy of these changes. Additionally, from an aquatic habitat and water quality perspective, the discharge of drainage waters into Delta waterways represents a poorly constrained source of pesticides, nutrients, and other ions, which may be important to consider in terms of ecosystem health, harmful algal blooms, and drinking water quality.

Authors

• Christina Richardson*⁺, University of California at Santa Cruz, cmrichar@ucsc.edu
• T. Kraus, USGS
• A. Paytan, UCSC
• H. Ly, USGS
• K. Nakatsuka, USGS
• J. Orlando, USGS
• J. Fackrell, USGS

* Presenting author
⁺ Early Career Award candidate

Abstract

In collaboration with the California Department of Water Resources (DWR), the U.S. Geological Survey (USGS) Pesticide Fate Research Group is monitoring a large suite of pesticides in the Yolo By-Pass that receives non-managed seasonal and local flow and managed flow pulses from agricultural drainage or the main stem of the Sacramento River. Augmented flow pulses are hypothesized to increase net positive flow during summer–fall in the Yolo By-Pass, thereby enhancing plankton availability in the Cache Slough complex. However, flow pulses may also result in unintended negative effects of increased pesticide levels that are transported through the Yolo By-Pass. In this study we evaluated pesticides in the Yolo By-Pass during the 2021–2023 water years and evaluated observed concentrations with respect to acres used for rice growth and streamflows. Water samples were collected by DWR personnel biweekly for two months between August and October at up to 7 sites. These samples were analyzed by the USGS for a suite of 178 current-use pesticides and pesticide degradates; these included a range of herbicides, insecticides, and fungicides. Fifty-two compounds were detected in water samples collected during the study, at concentrations ranging from below method detection limits to 4,538 nanograms per liter. The sum of average concentrations for pesticides that are used exclusively on rice were highest in samples collected in 2023, followed by samples from 2021 and 2022. Acreage dedicated to rice crops during 2023, 2021, and 2022 were 514,000, 471,000 and 256,000, respectively. Pesticide concentrations positively correlate with acreage of rice growth and daily mean discharge. These results can help us understand the impact of flow and changes in agriculture on pesticide occurrence and concentrations in the Yolo By-Pass and other areas of the Sacramento-San Joaquin Delta.

Authors

• Matthew Uychutin*⁺, U.S. Geological Survey, muychutin@usgs.gov
• James Orlando, U.S. Geological Survey California Water Science Center
• Michelle Hladik, U.S. Geological Survey California Water Science Center
• Corey Sanders, U.S. Geological Survey California Water Science Center
• Elisabeth LaBarbera, U.S. Geological Survey California Water Science Center
• Matthew De Parsia, U.S. Geological Survey California Water Science Center
• Laura Twardochleb, California Department of Water Resources
• Mackenzie Miner, California Department of Water Resources
• Eric Holmes, California Department of Water Resources
• Brittany Davis, California Department of Water Resources

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Across the Sacramento-San Joaquin Delta, wetland restoration efforts have been implemented, are under construction, or are being planned, with the explicit goals of providing habitat for native species and providing food web supplementation to benefit endangered species within these restored sites and in downstream habitats. Understanding how existing wetlands function is critical to informing adaptive management and the design of future wetland restoration sites. Documenting spatial and temporal trends in water quality, nutrients, and phytoplankton is a key part of evaluating wetland performance and can provide insights into how wetland design impacts hydrodynamics, water residence time, primary productivity, and habitat quality. Water-quality data collected using discrete sampling or continuous monitoring stations provides key information, but the spatial and temporal limitations of these data may not sufficiently characterize hydrodynamically, geomorphologically, and biologically variable wetland ecosystems. The Biogeochemistry Team at the U.S. Geological Survey California Water Science Center collected high-resolution water quality data in shallow wetland environments by equipping an inflatable kayak with a flow-through system and a suite of in situ instrumentation. This approach builds on USGS experience collecting high-resolution water quality, nutrient and phytoplankton data on larger boats in channels and deeper open-water habitats. The system was deployed as a proof-of-concept in the First Mallard Branch wetland on November 20, 2023. We will present pilot study results and demonstrate the spatial variability of parameters such as temperature, specific conductance, turbidity, dissolved oxygen, pH, phytoplankton abundance, and dissolved organic matter in this dendritic wetland system. The observational data collected using this approach can be used by modelers to validate and calibrate their models.

Authors

• Jesse Schroeder*⁺, USGS CAWSC, jschroeder@usgs.gov
• Katy O’Donnell, USGS CAWSC
• Hieu (Tommy) Ly, USGS CAWSC
• Patrick Dellwo, USGS CAWSC
• Jacob Brinkman, USGS CAWSC
• David Ayers, USGS CAWSC
• Tamara Kraus, USGS CAWSC

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

Across the Sacramento-San Joaquin Delta, wetland restoration efforts have been implemented, are under construction, or are being planned, with the explicit goals of providing habitat for native species and providing food web supplementation to benefit endangered species within these restored sites and in downstream habitats. Understanding how existing wetlands function is critical to informing adaptive management and the design of future wetland restoration sites. Documenting spatial and temporal trends in water quality, nutrients, and phytoplankton is a key part of evaluating wetland performance and can provide insights into how wetland design impacts hydrodynamics, water residence time, primary productivity, and habitat quality. Water-quality data collected using discrete sampling or continuous monitoring stations provides key information, but the spatial and temporal limitations of these data may not sufficiently characterize hydrodynamically, geomorphologically, and biologically variable wetland ecosystems. The Biogeochemistry Team at the U.S. Geological Survey California Water Science Center collected high-resolution water quality data in shallow wetland environments by equipping an inflatable kayak with a flow-through system and a suite of in situ instrumentation. This approach builds on USGS experience collecting high-resolution water quality, nutrient and phytoplankton data on larger boats in channels and deeper open-water habitats. The system was deployed as a proof-of-concept in the First Mallard Branch wetland on November 20, 2023. We will present pilot study results and demonstrate the spatial variability of parameters such as temperature, specific conductance, turbidity, dissolved oxygen, pH, phytoplankton abundance, and dissolved organic matter in this dendritic wetland system. The observational data collected using this approach can be used by modelers to validate and calibrate their models.

Authors

• Dulcinea Avouris*, USGS CAWSC, davouris@usgs.gov
• Emily Richardson, USGS CAWSC
• Katy O’Donnell, USGS CAWSC
• Jacob Brinkman, USGS CAWSC
• Hieu (Tommy) Ly, USGS CAWSC
• Crystal Sturgeon, USGS CAWSC
• Nick Framsted, USGS CAWSC
• Kavi McKinney, USGS CAWSC
• Erin Hestir, UC Merced
• Brian Bergamaschi, USGS CAWSC
• Keith Bouma-Gregson, USGS CAWSC
• Tamara Kraus, USGS CAWSC

* Presenting author

No poster image available.

Abstract

Various stressors due to climate change including sea-level rise and drought impact estuarine ecosystems and contribute to fluctuations in salinity levels. When there is a high salt concentration in an ecosystem, increased competition between salt ions and other compounds for interactions with water molecules reduces the amount of a chemical dissolved in water and may cause an increase in its ability to concentrate in the fat tissue of fishes. As a compound becomes more lipophilic (less water soluble), coastal organisms may be more sensitive to chemical exposure as uptake into the body can increase. Pesticides are chemical compounds commonly used for agricultural and household purposes, and they can enter estuarine ecosystems through runoff. To determine if there is a difference of pesticide toxicity at varying salinities, Menidia beryllina embryos at six days post fertilization (approximately 1-day pre-hatch) were exposed to sublethal levels of six pesticides (bifenthrin, chlorpyrifos, dicloran, myclobutanil, penconazole, triadimefon) at two salinities (5 PSU and 25 PSU) for 96 hours. Menidia beryllina (Inland silverside) are a euryhaline model species, which allows for the ability to observe stressor effects over a broad range of salinities. Behavior, growth, and gene expression are endpoints that will be analyzed for effects at sublethal exposure levels as impacts observed at early life stages of fish could have potential population effects due to organism fitness contributing to overall survival.

Authors

• Katherine Berreman*⁺, Oregon State University, Corvallis, OR, katherine.berreman@oregonstate.edu
• Sara Hutton, GSI Environmental Inc., Olympia, WA
• Scott St. Romain, Louisiana State University, Baton Rouge, LA
• Kevin Armbrust, Louisiana State University, Baton Rouge, LA
• Susanne Brander, Oregon State University, Corvallis, OR

* Presenting author
⁺ Early Career Award candidate

No poster image available.

Abstract

To collect spatially rich water quality, nutrient, and phytoplankton data across the entire Sacramento-San Joaquin Delta (Delta), the U.S. Geological Survey completed high resolution mapping surveys across the Delta in spring, summer and fall of 2018, 2020, 2021, 2022, and 2023. High-resolution data from these surveys provide detailed information about spatial and temporal variability that cannot be captured by discrete sampling or continuous monitoring stations. Each survey represents a snapshot in time which can be used for a variety of data analytics pathways and can help inform a wide range of research and management questions. For example, these data document Delta-wide nutrient gradients through different phases of the EchoWater resource recovery facility’s Biological Nutrient Reduction upgrade. When contextualized with management actions and extreme weather events (e.g., gate operations and droughts), we can explore links to phytoplankton abundance and distribution. We can identify point-source nutrient inputs, document the extent of harmful algal blooms, demonstrate rapid nutrient drawdown associated with phytoplankton blooms, and calculate water age. These data are also being used by modelers to build, calibrate, and validate linked hydrologic and biogeochemical models. Individual researchers may delve into data from specific areas of interest (e.g., a river reach or slough) to gain insights into the water quality and health of the lower food web in their target locations. Remote sensing models can also be improved upon with these spatially rich data. In this poster presentation, we will highlight some of the ways these data are being used and some of the findings.

Authors

• Katy O'Donnell*, kodonnell@usgs.gov
• Emily T. Richardson (USGS)
• Kyle Nakatsuka (USGS)
• Jacob Brinkman (USGS)
• Nicholas Framsted (USGS)
• Jeniffer Soto-Perez (USGS)
• Crystal Sturgeon (USGS)
• Elizabeth Stumpner (DWR, formerly USGS)
• Keith Bouma-Gregson (USGS)
• Brian A. Bergamaschi (USGS)
• Tamara E.C. Kraus (USGS)

* Presenting author