This project aims to quantify the impacts of common reed (Phragmites) invasion on community structure and ecosystem function during early stages of tidal restoration in wetlands. The study will focus on the Tule Red Tidal Restoration site in Suisun Marsh. The research aims to produce a conceptual model that will describe habitat structure, invertebrate communities, and predator use of wetlands affected by Phragmites invasion. The conceptual model resulting from this study will guide future predictions of wetland response to invasion and to develop mitigation strategies. Data collected will also support food web models and the understanding of invasive plants as stressors, as well as foster translational science to the management community.
Description We propose to develop an eDNA metabarcoding protocol to complement existing IEP monitoring surveys and assess the effects of management activities such as habitat restoration or flow alteration. We will develop a reference sequence database for native and invasive fish, mussels, and other macroinvertebrates present in the San Francisco Estuary (SFE). We will optimize a molecular and computational pipeline for metabarcoding and ground truth the method against three SFE monitoring efforts, each using different sampling gear. We will investigate the relationship between eDNA sequence read count and fish biomass or abundance (EDSM survey). Finally, we will determine the ability of metabarcoding to detect fish and macroinvertebrate assemblages across large and small spatial scales and over time. Need Our overarching goal is to develop a non-invasive, low cost monitoring tool that can be used in conjunction with existing IEP monitoring programs or used alone to assess biological community composition at locations of interest in the SFE. This proposal is related to the 2020 - 2024 IEP Science Strategy by creating a new monitoring tool that can assist in two main areas: 1) Restoring Bay-Delta native fishes and community interactions and 2) assessing effects of flow alteration on Bay-delta aquatic resources. Broadly, this study will inform management decisions by supporting and augmenting existing monitoring surveys in the SFE. It will also lead to a richer and more complete understanding of SFE ecology. This study is not explicitly required by law or agreement, and to our knowledge is neither a recommended action nor a result from an IEP review or synthesis effort. Objectives Objective 1: Develop robust molecular methods and a computational pipeline for detection of SFE fish and macroinvertebrates by eDNA metabarcoding of water samples. Objective 2: Compare eDNA metabarcoding head-to-head with existing and historical monitoring data from three ongoing ecological surveys using diverse conventional sampling gear and evaluate accuracy of fish abundance and biomass estimates from eDNA metabarcoding data. Objective 3: Evaluate factors that influence eDNA detection of species of interest (e.g. rare or invasive species) and suites of species (e.g. benthic fishes and invertebrates) on two spatial scales, within and between habitats, along with temporal variation.
Description The overarching goal of this project is to determine if predation by piscivorous fishes is an important explanatory driver of survival of juvenile Chinook Salmon emigrating through the north Delta. To achieve this goal, we seek to determine if variation in reach-specific characteristics of predation dynamics covary with survival of acoustictagged juvenile Chinook Salmon collected during the study period. This will be accomplished by comparing reach-specific characteristics of the piscivore community and its observed and modeled consumption of juvenile Chinook Salmon across a range of environmental conditions. Need This is not a mandated study but it addresses an important research need. Objectives: How does the piscivore community (species composition, size structure, and abundance) vary across specific migratory pathways (river reaches) in the North Delta? To what extent do environmental conditions (e.g., water temperature, turbidity, and discharge) control the consumption of juvenile Chinook Salmon? Do characteristics of the predator community explain variation in survival of acoustic tagged salmon collected during the study period?
The Environmental Monitoring Program (EMP) began in 1975 to conduct baseline and compliance monitoring of water quality, phytoplankton, zooplankton, and benthic invertebrates in the San Francisco Bay-Delta estuary. This monitoring program was designed to track the impact of water diversions to the State Water Project (SWP) and Central Valley Project (CVP) on the Bay-Delta. In the decades since, EMP scientists have monitored these constituents at fixed and floating stations throughout the estuary and ensured compliance with state and federal mandates such as Water Right Decision 1641 (D-1641). In the years and decades since its inception, EMP has become one of the cornerstones for scientists' and managers' understanding of the pace and pattern of change in this critical ecosystem. By sampling water quality and biological communities concurrently, EMP has created a dataset that is uniquely useful in better understanding causal connections between physical, biological, and biogeochemical processes.
The Delta Juvenile Fish Monitoring Program (DJFMP) has monitored natural-origin and hatchery-origin juvenile Chinook Salmon (Oncorhynchus tshawytscha) and other fish species within the San Francisco Estuary (SFE) since 1976 using a combination of midwater trawls and beach seines. Since 2000, three trawl sites and at least 58 beach seine sites have been sampled weekly or biweekly within the SFE and lower Sacramento and San Joaquin Rivers. The main objectives of the DJFMP are: 1. Document the long-term abundance and distribution of juvenile Chinook Salmon in the Delta. 2. Comprehensively monitor throughout the year to document the presence of all races of juvenile Chinook Salmon. 3. Intensively monitor juvenile Chinook salmon during the fall and winter months for use in managing water project operations (Delta Cross Channel gates and water export levels) on a real-time basis. 4. Document the abundance and distribution of Steelhead. 5. Document the abundance and distribution of non-salmonid species.
The CDFW Fish Restoration Program will collect fish and invertebrate data near existing and planned tidal wetlands. These data will provide information on how fish and invertebrate communities change pre-/post-restoration. While collecting these data, the variability of invertebrate catches will be assessed for each gear type to determine the optimal number of samples per sampling site.
Under the 2008, 2019, 2024 State Water Project/Central Valley Project Joint Operations Biological Opinion from United States Fish and Wildlife Service, 2009, 2019, 2024 National Marine Fisheries Service, and 2009, 2020, and 2024 State Water Project Incidental Take Permit, Department of Water Resources (DWR) is required to restore >8,000 acres of tidal wetlands in the Sacramento-San Joaquin Delta (Delta) and Suisun Marsh to improve habitat and food web resources for threatened fishes. The Fish Restoration Program is responsible for biological monitoring in these restored tidal habitats to assess their success for providing habitat and food web benefits for at-risk native fishes.
Assess the food web resources (nutrients, phytoplankton, zooplankton, and macroinvertebrates) associated with pre- and post-restoration tidal wetlands, as well as with existing reference wetlands
Assess the fish community of restoring wetlands including use by rearing salmonids and characterization of the predator and competitor communities
The Wetland Regional Monitoring Program (WRMP) Fish and Fish Habitat Monitoring project is a collaborative effort to track biological responses to tidal wetland restoration in the San Francisco Estuary. Monthly sampling is conducted across a network of benchmark, reference, and project restoration sites in the South Bay and North Bay, with the goal of evaluating how wetland restoration influences fish assemblages, habitat use, and ecological condition.
The study uses primarily otter trawls to monitor fish and macroinvertebrate communities. Standardized field methods align with those used in long-term monitoring programs to ensure comparability and data integration across regions. Environmental data, including water temperature, salinity, and dissolved oxygen, are collected in tandem with biological sampling to assess habitat quality and seasonal dynamics.
The program addresses WRMP Guiding Question #4: How do policies, programs, and projects to protect and restore tidal marshes affect the distribution, abundance, and health of fish and wildlife? The data support adaptive management, regulatory compliance, and science-based restoration planning by identifying key habitats, tracking restoration performance, and detecting regional patterns in species composition and abundance over time.
Invasive aquatic vegetation (IAV) is a threat to aquatic ecosystems worldwide, leading to a major loss of biodiversity and extensive damages and costs to human uses of those ecosystems. The Sacramento-San Joaquin River Delta (the “Delta”) is the hub of California’s water system, supporting over 35 million water users and a $54 billion agricultural industry. The Delta reform act mandates management decisions meet both water supply needs while maintaining the ecological function of the system. The Delta is a global biodiversity hotspot, and the focal point of $750-$950 million in restoration. It has also been called one of the most invaded estuaries in the world. Over the past 15 years, submerged and floating IAV have more than doubled in extent, threatening water supply and ecosystem health of the Delta. There is mounting evidence that herbicide treatments are not effective, and that water management actions, and wetland restoration may be having huge impacts on IAV. This presents both a risk to increasing IAV, but also an opportunity to prevent and even effectively combat IAV through considered water management actions and better restoration planning, meeting the state’s co-equal goals of water security and Delta ecosystem conservation.
This project will meet the needs of multiple state agencies by advancing operational Earth observation-based monitoring program for community-level submerged aquatic vegetation (SAV) and genus-level floating aquatic vegetation (FAV) and modeling tools to enable the Delta management community to assess the effect of previous management actions on IAV and forecast the effects of future actions to inform multi-agency decision making. Specifically, this work will 1) Operationalize IAV class mapping using Sentinel-2 satellite imagery, 2) Finalize and validate species distribution Models (SDM) for SAV community and FAV at genus-level to assess the impacts of previous water actions on IAV and predict IAV distribution in future scenarios, 3) Co-design IAV-based performance metrics to inform future actions.
The proposed project fills a critical data gap in monitoring for state and federal agencies and stakeholders by implementing the first sustainable mapping effort for IAV. Monthly and seasonal estimates of SAV and FAV coverage will enable the Delta Stewardship Council to improve their performance metrics for evaluation of the Delta Plan and will help the Interagency Ecological Program assess whether management is meeting the co-equal goals for the Delta. Species distribution models will enable Department of Water Resources to evaluate how previous restoration flow actions have affected the spread and persistence of IAV and incorporate what they learn into future Structured Decision Making to better account for negative consequences of IAV when setting future restoration targets and implementing actions.
Water primrose (Ludwigia spp.) is a highly invasive, non-native floating macrophyte in the Delta. In recent years, water primrose has extended its niche into marsh habitat, causing extensive mortality of marsh macrophytes including tules and cattails. The goal of this project is to determine whether the growth strategy of water primrose, its allelopathic properties, or factors related to plant community structure are the cause of marsh loss following water primrose invasion in the Delta. Part of this study will identify and map the marshes most vulnerable to loss and quantify the spatial trajectory of marsh loss during the past 15 years. The ultimate benefit will be an improved understanding of the water primrose invasion processes in the Delta, which can be used to prioritize herbicide treatment of this highly invasive plant in marshes most vulnerable to invasion and with the highest habitat value.
Objectives:
Since 2015, the DIISC Team has organized a biennial Delta Invasive Species Symposium. The symposium is a forum for Delta managers, researchers, and decision-makers to meet, share and synthesize information, and communicate best practices and lessons learned. https://deltaconservancy.ca.gov/diisc-team-activities/
This guide is intended to give land managers an introduction to managing invasive aquatic vegetation (IAV) in tidal wetland habitats, whether the site is established, has been recently restored, or tidal reconnection will soon occur. It addresses submerged aquatic vegetation (SAV), floating aquatic vegetation (FAV), and emergent aquatic vegetation (EAV). It compiles knowledge from land managers in the Delta and members of the Delta Interagency Invasive Species Coordination Team (DIISCT), whose purpose is to foster communication and collaboration among California state agencies, federal agencies, research and conservation groups, and other interested parties that detect, prevent, and manage invasive species and restore invaded habitats in the Delta. The authors hope this guide functions like asking an experienced colleague for recommendations as you start to consider your site’s IAV management. https://deltaconservancy.ca.gov/iav-quick-start-guide/
Preventing the establishment of new invasive species through early detection and rapid response (EDRR) is the most effective and efficient way to limit the negative impacts of invasive species on the Delta. In 2021, the DIISC Team lead a review of the different EDRR resources in the Delta and drafted an EDRR coordination table.
Invasive aquatic macrophytes (aquatic weeds) cover increased dramatically in the Sacramento-San Joaquin Delta (Delta) during the 2013-2015 drought and the 2021-2023 drought. This trend toward increasing dominance of these invasive aquatic weeds has profound implications for delta/marsh habitat, as aquatic weeds are known to significantly alter the physical environment by slowing water velocities, increasing water clarity, providing habitat for invasive fishes, and reducing open water habitat. These habitat effects are thought to negatively impact the endangered Delta Smelt and other pelagic species that rely on turbid, open water habitat. During the drought of 2021- 2023, aquatic weeds have continued to spread into new habitats, therefore there is an urgent need to identify effective control measures, which requires increased understanding of ecosystem responses to drought and associated environmental conditions in the waterways (e.g., water temperature, flow rates, turbidity, etc.), and specific control measures.
The work covered in this contract includes the 2021-2023 Emergency Drought Salinity Barrier Monitoring Plan mandated under DWR’s Incidental Take Permit. Research has focused on understanding invasion patterns in Franks Tract and contrasting them with patterns in channels surrounding Liberty Island and restoration sites. We also analyze Suisun marsh to assess the condition near the salinity drought barrier on Montezuma Slough, and its impacts across the length of Montezuma Slough and relate observed patterns to salinity conditions in Suisun Slough.
Extensive field work has been conducted throughout the Delta and in Suisun Marsh to acquire data that is used to train and evaluate remotely sensed maps of aquatic weed distribution and link these to measurements of water quality. This project extends the time period of continued mapping of aquatic vegetation in the Delta through summer of 2027, for a time series that goes back to 2004, covering 19 years of high spatial resolution hyperspectral imagery data. This dataset now encompasses the full range of hydrologic conditions that extend from wet years to extremely dry years which can potentially form the basis for interpreting causal relationships and changes in trait distributions of aquatic weeds. Aquatic weed mapping combined with an extensive field campaign within the Suisun Marsh extends the Suisun time series to seven years. This growing time series of vegetation maps for both the Delta and Suisun Marsh can be leveraged to look at the evolution of tidal wetland restoration sites developed by DWR’s Fish Restoration Program (FRP) as part of the Incidental Take Permit. This analysis covers construction to current time period to see if different restoration strategies (pre-planting, no pre-action, treating invasive species outside the site, etc.) have an impact on the growth and maturity of a site, invasibility, etc. Additionally, the full time series will be evaluated for trends related to weather/climate, water conditions, and management actions.
The California Department of Parks and Recreation, Division of Boating and Waterways (DBW) operates a control program for both floating and submerged IAV. This project is an IEP Synthesis effort that will integrate a historical and ongoing dataset of the Delta IAV coverage and DBW IAV treatment records for the past 14 years. This study seeks to determine if treatment efficacy differs across space (e.g., different habitat types) and time. It will assess the impact of IAV control effort on the distribution, growth rate, spread and persistence, and species richness and community composition of the IAV communities. Gaining such understanding on the relationship between IAV treatment and IAV distribution, coverage, and species composition is an urgent management issue for the Delta, given the sharp rise in coverage of IAV from 9000 acres in 2004 to 12,500 acres in 2014 and its likely impact on the shallow-water habitat.
The objectives of this study are:
1. What are the rates and patterns of spread for floating IAV? Do the rates of spread into water or marsh differ? Where do these floating IAV persist and what mechanisms can be linked to their ability of persistence? If there are specific locations that promote persistence, for example over-wintering nurseries, could they be targeted for removal?
2. Has treatment for both water primrose and water hyacinth been successful in reducing species cover over the last 15 years? If so, was treatment effective in reducing density, reducing growth rates, slowing down expansion, and therefore changing distribution of target species? Does treatment efficacy change over different habitats and through time?
3. Does herbicide control of target submerged IAV species reduce density, growth rates, slow down expansion and persistence, and change submerged community composition towards native species? Does treatment efficacy change over different habitats and through time? Does it change the patch size and distribution?
