The Science and Management of the San Francisco Estuary (hosted by AFS)

The San Francisco Bay-Delta is one of the most intensively studied estuaries in the world, including over four decades of fish and water quality monitoring. Since the estuary is the water supply for 25 million people and a multi-billion dollar agriculture industry, the region is at the epicenter of pervasive conflicts between human and environmental needs in the western United States. The objective of this symposium is to highlight some of the biggest fisheries issues, and the ways that the latest science is being used to support ecosystem management. The focus of the symposium will be two imperiled species, Delta Smelt and Chinook Salmon, which are heavily managed throughout much of their life cycles. The session will be of interest to fisheries scientists from other regions that wish to become more familiar with western water issues, and to regional experts looking to see some of the latest research. The session will include an introduction to the system and the major fish resources and a companion overview of some of the novel ways that monitoring is used for management. Talks will highlight three of the major fish issues, water diversion entrainment, flow management, and habitat restoration. Since the system is one of the most heavily invaded estuaries on the planet, the session will cover management of invasive species. Additional presentations will also discuss the current and potential future ways that hatchery fish are used for management.

8:00AM Recent Progress in Salmon Science in the San Francisco Estuary
  Anna Sturrock, Corey Phillis, Stephanie Carlson, Ted Sommer, Rachel C. Johnson, PhD
Today’s San Francisco Bay-Delta (‘Delta’) has lost most of its historically diverse wetland habitats and is dominated by non-native piscivorous fishes, yet all Central Valley salmon must navigate it in order to reach the ocean. Despite being a well-studied system, little is known about salmon rearing behaviors, growth rates, and survival probabilities through this common pathway. Here, we provide a brief overview of recent studies leveraging traditional monitoring datasets with non-traditional tools to garner new insights into the way salmon use this anthropogenically-altered environment. We then focus on a study quantifying the contributions of different populations and emigration behaviors (early vs. late) successfully entering the ocean during droughts and floods. Using otolith (“earstone”) strontium isotope and daily increment measurements, we reconstructed the origins, rearing histories, and freshwater growth rates of juveniles entering, residing in, and leaving the Delta in 2014-17. Multiple lines of evidence suggest that early and late migrants are more strongly selected against during outmigration, potentially compressing ocean arrival timings and increasing vulnerability to match-mismatch events. In a changing climate, there is a growing need to quantify – and monitor – processes that erode stock diversity to help design management actions that promote viable and resilient salmon populations.
8:20AM Uncovering the Complex Life Histories of a “Stupid Little Fish” to Improve Freshwater Management in the San Francisco Estuary.
  James Hobbs, Levi Lewis, Christian Denney, Naoaki Ikemiyagi, Bush Eva, Wilson Xieu, Feng Zhao, Wendy Chen
The Delta Smelt (Hypomesus transpacificus) was once an abundant pelagic forage fish endemic only to the upper reaches of the San Francisco Estuary and served as the indicator of ecosystem health, but is now rarely observed in long-term monitoring surveys, signifying its trajectory towards extinction. Its demise has been blamed on a multitude of anthropogenic impacts and regulations imposed to protect the species form the epicenter of California’s water-wars. Its frequent impingement and disruption of California’s water supply has caused it to be known as the “stupid little fish” in the halls of congress. Here, we present results from 20-years of otolith based studies investigating how life history diversity and growth have responded to freshwater flow management, a changing foodweb, declining turbidity and a warming climate. We use these results in hopes of improving management strategies to avoid extinction in the wild and develop an effective plan for recovery for this iconic species.
8:40AM Introduction to the San Francisco Estuary and Its Fishes
  Steven Culberson
The Upper San Francisco Estuary can be considered to be a series of embayments arranged along a tidal riverine axis of increasing salinity downstream to the sea. Historic geomorphologic and hydrologic dynamism provide the basis for complex life history strategies for suites of species that occupy California’s Mediterranean climate and extensive Central Valley. Modern land use and water resource development have had wide-ranging and lasting effects on habitats and landscape connectivity over the last century, and human management of the ecosystem has put continuing ecosystem services at risk. This introductory talk will provide an ecological and anthropologic setting for the talks that follow, placing into proper focus the extent and degree of manipulation with which special status species in the system have had to contend. Challenges to successful natural resources management will be identified, and a brief description of the sociopolitical environment in the Estuary will be articulated.
9:00AM From Data to Decisions: How Fish Monitoring Informs Water Management in the Largest Estuary on the West Coast
  Brian Schreier
The San Francisco Estuary (SFE) is a heavily managed estuary/river system at the heart of one of the world’s largest water distribution systems providing water to four million acres of farmland and 25 million people. To inform this management and its consequences to the ecosystem, the SFE also contains a robust science monitoring enterprise coordinated under the Interagency Ecological Program. Twenty-two long-term monitoring programs plus numerous other research and monitoring initiatives, spanning water quality, hydrology, lower trophic productivity, and multiple fish species, provide immense amounts of data to water managers. All of this data is funneled through a patchwork of technical teams and advisory groups, culminating in real-time operational decisions affecting the timing and amount of water being exported to cities and agricultural areas south of the SFE. These “data to decisions” processes primarily focus on three regulated aspects of the SFE ecosystem: water quality, Chinook Salmon (Oncorhynchus tshawytscha), and Delta Smelt (Hypomesus transpacificus). Among these, water operations decisions based on protections for Delta Smelt are perhaps the most contentious. The compliance monitoring framework informing Delta Smelt management will be discussed, as well as the process for synthesizing these data streams into real-time decisions informing infrastructure operations.
9:20AM Management of Delta Smelt Entrainment May be Necessary, but Is It Sufficient?
  William E. Smith, Ken B. Newman, Lara Mitchell, Leo Polansky
Past management of Delta Smelt, an endangered Osmerid endemic to the San Francisco Estuary, has placed high conservation value on minimizing population losses from water diversions to supply southern California with irrigation and drinking water. Hydrodynamic quantities that index advective flows, thought to influence entrainment risk into water export projects, are actively managed during the Delta Smelt spawning season. Effective future management of natural resources requires periodic assessment of past management actions, and quantitative assessment must include uncertainties in processes linking vital population rates to management actions and in observations of population effects. The Delta Smelt Life Cycle Model (LCM) is an effort to assess present and past Delta Smelt population status, quantify drivers of population dynamics, and provide quantitative support for Delta Smelt conservation policy while accounting for uncertainty. The LCM describes processes of entrainment mortality as a function of managed hydrodynamic quantities, natural mortality, and reproduction among 6 life stages. Results indicated a significant reduction in entrainment mortality around the time that contemporary management of entrainment loss began, and this was associated with long-term trends in spawning season advective flows into the South Delta. Concurrently, natural mortality of postlarvae increased and abundance of all lifestages declined.
09:40AM Break
1:10PM Assessing the Response of Endangered Delta Smelt to High Flows in 2017 in the Sacramento-San Joaquin Delta, California: An Interdisciplinary, Multi-Agency Approach
  Larry Brown, Brian Mahardja
Management of water for human and environmental purposes can lead to conflict and is one of the most contentious issues in the Sacramento-San Joaquin Delta, California. The importance of outflow to Delta Smelt (Hypomesus transpacificus) remains one of the central questions for resource managers. In 2016, the Interagency Ecological Program established the Flow Alteration (FLOAT) Project Work Team as a forum for developing a better understanding of how flow management actions affect the San Francisco Bay-Delta ecosystem. In water year 2017, historic winter precipitation and snowpack resulted in high flows expected to favor Delta Smelt but the population showed no apparent increase. To better understand what happened in 2017, the FLOAT Management, Analysis, and Synthesis Team (MAST) was formed and includes experts on Delta Smelt-related topics tasked with conducting data analysis and synthesis. Analyses to date suggest that warm summer water temperatures may have been a key factor limiting Delta Smelt growth and survival in 2017. Because air temperature rather than flow is the primary factor controlling water temperature, this would be an important finding for Delta Smelt conservation. Given that humans cannot control air temperature at the ecosystem scale, designing effective Delta Smelt restoration strategies will be challenging.
1:30PM Evaluation of a Large Scale Flow Manipulation to Upper San Francisco Estuary: Response of Habitat Conditions for an Endangered Native Osmerid
  Ted Sommer, Louise Conrad, Michal Koller, Michael Koohafkan, Michael MacWilliams, Aaron Bever, Michael Beakes, Burdi Christina, April Hennessy, Denise Barnard
While flow is known to be a major driver of estuarine ecosystems, targeted flow manipulations are rare because these habitats are extremely variable, and because the necessary infrastructure is rarely available. During summer 2018 we used a unique water control structure to direct a managed freshwater flow pulse into Suisun Marsh, the one of the largest tidal marshes on the west coast of the United States. The action was designed to support habitat conditions for the endangered Delta Smelt Hypomesus transpacificus. The basic approach was to operate the Suisun Marsh Salinity Control Gates (SMSCG) to direct 130 TAF pulse of Sacramento River flow into Suisun Marsh during August, a critical time period for juvenile Delta Smelt rearing. Three-dimensional modeling of the action showed that directing a freshwater flow pulse into Suisun Marsh substantially increased habitat area for Delta Smelt. Field monitoring of the action the resulting turbidity and lower trophic level conditions in Suisun Marsh were significantly better than upstream habitat in the lower Sacramento River. Fish monitoring data suggest that small numbers of the Delta Smelt colonized Suisun Marsh from the Sacramento River during the action, further supporting our hypothesis that augmented flows would benefit this rare species.
1:50PM Did Lower Salinity Mean Different Fishes? a Look at the 2018 Aquatic Community in Suisun Marsh.
  Michael Beakes, Louise Conrad, Cory Graham, James White, John Durand, Ted Sommer
The 2018 Suisun Marsh Salinity Control Gate action was designed to improve access to high-quality habitat for Delta Smelt (Hypomesus transpacificus) throughout Suisun Marsh in California’s San Francisco Delta. The action involved manipulating gate operations between tidal cycles to decrease salinity in the marsh. We sought to evaluate if decreasing salinity in Suisun Marsh altered the local aquatic community. We used a combination of NMDS analyses and circular statistics to evaluate the magnitude and characteristics of community change using long-term monitoring data collected within Suisun Marsh and adjacent regions in July and August. We found the community in Suisun Marsh and adjacent regions changed significantly within and across water-year types. Within a region and water-year type the community historically shifted significantly towards more brackish-tolerant species as the summer progressed from July to August. However, the 2018 July-to-August community shift differed from historical trends with protracted residence of some freshwater species and a marked decline in some brackish-tolerant species; the magnitude and variability of these changes differed by habitat type. We posit the observed community changes were driven by a combination of behavioral responses to lower-salinity conditions and hydrodynamic displacement from Suisun Marsh Salinity Control Gate operations.
2:10PM Assessing the Effectiveness of Tidal Wetland Restoration for Supporting Native Fish
  Stacy Sherman
The Sacramento-San Joaquin Delta was once a vast expanse of tidal wetlands and dendritic channels that supported large populations of endemic Delta Smelt and rearing Chinook Salmon. Greater than 90% of tidal wetland habitat was “reclaimed” by the early 1900’s, and subsequent introductions of myriad invasive species and contaminants, as well as altered hydrology, have created a novel low-productivity ecosystem in which native fish populations have not fared well. Tidal wetland restoration is gaining prominence as a mitigation measure intended to provide fish habitat and bolster the food web in adjacent channels. To gauge the effectiveness of this strategy in such an altered estuary, and to enable adaptive management of restoration design, a robust monitoring program is essential. The California Department of Fish and Wildlife led an inter-agency effort to: 1) Create conceptual models to guide hypothesis development for restoration outcomes; 2) Develop a framework for project-specific monitoring plans using similar or complementary hypotheses; and 3) Provide detailed standard operating procedures for recommended monitoring methods and data management. Prior to large-scale restoration, we are collecting baseline data on a set of future project and reference sites and are promoting our methods and data sharing to other projects in the region.
2:30PM Experimental Quantification of Piscivore Density and Habitat Effects on Juvenile Chinook Salmon Survival and Movement in a Tidal Freshwater Delta.
  Steven Zeug, Michael Beakes, Lenny Grimaldo, Jason Hassrick, Alison Collins, Shawn Acuna
Predation by non-native piscivores is suspected of contributing to poor survival of juvenile Chinook Salmon (Oncorhynchus tshawytscha) in the Sacramento-San Joaquin Delta. However, estimation of survival occurs over large spatial scales complicating attempts to understand the context of predation events. To begin addressing this uncertainty, experimental enclosures were used to test relationships between Largemouth Bass (Micropterus salmoides) density and habitat type on Chinook Salmon survival. Three contiguous enclosures were deployed in a tidal channel of the delta during spring 2018. Enclosures were separated with mesh sizes that allowed salmon, but not Largemouth Bass, to move between enclosures. Survival and movement among enclosures was monitored with a series of PIT tag antennas between each enclosure. The first experiment varied piscivore density (3, 6, or 12 Largemouth Bass) and the second experiment varied habitat type while predator density was held at the median level. Habitats were submerged aquatic vegetation (SAV), dock pilings and no habitat. Thirty five PIT tagged salmon were then introduced into each enclosure. Three replicates of each experiment were performed with treatments rotated among each enclosure. Largemouth Bass density had little support as an explanation of the data whereas survival was significantly reduced in the presence of SAV.
2:50PM Refreshment Break
3:20PM Science and Management of Invasive Aquatic Vegetation to Support Fish Habitat in the Sacramento-San Joaquin Delta
  Louise Conrad, Nick Rasmussen, Wright Hailey, Shruti Khanna, Tamara Kraus, Jeffrey Caudill
Invasive aquatic plants are a daunting management issue in the Sacramento-San Joaquin Delta, covering an estimated 25% of waterways, with multiple adverse effects (reduction of open-water habitat, promotion of predatory non-native fishes). Since the early 1990s, California State Parks has operated an herbicide-based control program. In 2017, we initiated an experiment to compare two treated and untreated sites within the habitat range of the endangered and endemic Delta Smelt. We quantified effects of herbicide treatment on submerged aquatic vegetation, water quality, plankton, and fishes. After two years of study, we found that treatment had no lasting effects on the submerged vegetation biomass or any other environmental metrics. Measured herbicide concentrations over the tidal cycle suggest this lack of a treatment effect may be due to rapid decreases in concentrations with tidal change. The fish community in these densely vegetated habitats is dominated by Largemouth Bass and other non-native centrarchids. During a seasonal drop in vegetation density, we observed an increase in native fishes, primarily in Sacramento Suckers, though more study is needed to demonstrate this as a reliable response. Overall, our results raise broad questions about appropriate treatment approaches in tidal, estuarine systems that need effective control of invasive vegetation.
3:40PM Genetic Approaches Informing Fish Management Decisions in the San Francisco Estuary
  Melinda Baerwald
The recent rapid innovation in genetic technologies has created powerful new tools for science-based decision-making. Some of these tools have already proven their utility in the highly dynamic San Francisco Estuary, where monitoring and management needs shift over time. Multiple recent and on-going genetic studies have provided critical and unique data that have informed decision-making for the recovery and management of vulnerable fish species (e.g. Chinook Salmon and Delta Smelt). In this presentation several recent informative case studies will be highlighted, including 1) genetic assessment of parentage and reproductive success in wild and captive populations, 2) environmental DNA detection of species in turbid tidally influenced water, and 3) genetic management of a captive refuge population. The presentation will also examine how genetic approaches are enabling more accurate and efficient taxonomic resolution (e.g. species, hybrids, salmon run types), which is a vital metric for many water management decisions and conveyance activities in California. Finally, prospects for genetics-informed management in the San Francisco Estuary will be explored with an emphasis on emerging genetic technologies.
4:00PM Planning a Release: Using Captive Bred Delta Smelt for Population Supplementation in the Face of Extinction
  Daphne Gille, Melinda Baerwald, Amanda Finger, Tien-Chieh Hung, Bryan Barney, Richard E. Connon, Dennis Cocherell, Nann Fangue, Andrea Schreier, Evan W. Carson, Nicole Kwan, Brian Schreier, Ted Sommer
The Delta Smelt (Hypomesus transpacificus) is an endemic osmerid in the San Francisco Estuary. The species is California and federally listed and abundance indices nearing zero indicate that extinction risk is high in the absence of intervention. A refugial Delta Smelt population at the University of California Davis Fish Conservation and Culture Laboratory could be used to supplement the dwindling wild population. However, critical knowledge gaps in Delta Smelt biology and the safety and efficacy of releasing cultured Delta Smelt into the Estuary have prevented such action. Several studies have been initiated to address these gaps. A draft Hatchery and Genetic Management Plan was crafted to set forth recommendations for a population supplementation plan, risk aversion measures, and monitoring to measure program success. Cages designed and constructed specifically for Delta Smelt were tested in the field using cultured fish, with resulting high survival. Molecular pathogen screening of wild and cultured Delta Smelt assessed the potential for pathogen transmission with supplementation. To limit potential domestication selection, methods to physically mark and in situ spawn fertilized Delta Smelt eggs were evaluated. Results of the studies presented here will enable managers to make informed decisions about the future supplementation of Delta Smelt.
4:20PM Density and Distribution of Piscivorous Fishes in the Sacramento – San Joaquin Delta
  Christopher Loomis, Mark Henderson
In this study I present a novel method to assess predator fish populations across the southern Sacramento-San Joaquin Delta using DIDSON acoustic cameras and analyze the environmental associations that form the landscape and fine-scale distribution of predatory fishes. I found that using mobile DIDSON acoustic cameras can be a user friendly method to enumerate predator fishes in a non-disruptive manner; however, factors affecting detection including environmental conditions and habitat complexity should be evaluated to refine these methods. Additionally, species differentiation of DIDSON footage would benefit from a larger library of acoustic footage of known predator fish. I found that predator fish distributions were primarily driven by spatial and structural habitat components with little evidence of temporal trends. Landscape-scale distribution was primarily driven by channel sinuosity, variation in depth, and the number of patches of submerged aquatic vegetation (SAV) in a reach. On a fine-scale, predators were more likely to be found near shallow, littoral habitats, SAV, and human-made structures. These results both provide guidance on how to implement a new survey method to assess the abundance of juvenile salmon predators in the Delta and indicate that reduction of invasive aquatic plants could decrease the abundance of these predator populations.
4:40PM A Tale of Two Gobies: Non-Native Tridentigers in San Francisco Bay
  Daniel Chase, Erin Flynn, Anne E. Todgham
Establishment of non-native species creates unique challenges for recovery of native fishes and can alter regional ecosystems by creating novel assemblages of organisms. San Francisco Bay, an estuarine ecosystem that is one of the most invaded aquatic regions in the world, supports several non-native goby species. Two of these species from the genus Tridentiger, shimofuri goby (T. bifasciatus) and chameleon goby (T. trigonocephalus), have become widely established within the San Francisco Bay. The phenotypic similarity between these two species has resulted in confusion with identification and distribution for each, yet these species present different threats to native fishes due to their physiological capabilities. Shimofuri goby had become widely distributed throughout San Francisco Bay, the Sacramento-San Joaquin Delta, and has even used the state water infrastructure to invade Southern California. Chameleon goby on the other hand, has a more restricted range in the state. This talk will provide an overview of each species, their history and distribution in California, along with some of the unique challenges these species pose for resource managers. Findings investigating the genetic relationship of these two species in San Francisco Bay, along with field sampling results that may update shimofuri goby habitable areas, will be presented.

Organizers: Ted Sommer
Supported by: Ted Sommer, AFS Fish Habitat Section

Location: Reno-Sparks CC Date: October 3, 2019 Time: 8:00 am - 5:00 pm