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  • Title

    Soil type as a driver of agricultural climate change response in the Sacramento-San Joaquin Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description This research project aims to increase understanding of how iron-rich peatland soils cycle carbon, nitrogen, and phosphorus in the delta and establish how carbon and nitrogen biogeochemistry and greenhouse gas emissions vary with management practices and crop type. It also explores how a drier future climate will influence biogeochemistry and greenhouse gas emissions in iron-rich soils and how to best adapt land management practices. The goal of this research is to identify agricultural practices that can generate a portfolio of climate change adaptation and greenhouse gas mitigation strategies for delta farmers. The greenhouse gas data collected as part of this research also helped to generate increasingly accurate emission offset credits for potential wetland restoration projects in California’s Cap-and-Trade program.
    Science topics Agriculture, Carbon, Nitrogen, Phosphorous, Soil
    Updated November 17, 2022
  • Title

    Effect of temperature and salinity on physiological performance and growth of longfin smelt: Developing a captive culture for a threatened species in the Sacramento- San Joaquin Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description This research project aimed to improve understanding of the physiological requirements for survival and reproduction across the entire life history of longfin smelt (from egg to larvae to juvenile to reproducing adult). The overall goals of this project were to assist in developing a captive longfin smelt culture and assess longfin smelt responses to multiple stressors across all life stages, which has been difficult because of extremely low (<10%) larval survival of these fish.
    Science topics Delta Smelt, Longfin Smelt, Salinity, Temperature
    Updated November 17, 2022
  • Title

    Identifying the Causes of Feminization of Chinook Salmon in the Sacramento and San Joaquin River System

    Lead University of California - Berkeley [UC Berkeley]
    Description Purpose was to assess the potential importance of endocrine-disrupting chemical contaminants to salmon and other resident speices of waters that are discharged into the San Francisco-San Joaquin Delta.
    Science topics Chinook Salmon
    Updated April 29, 2022
  • Title

    The Transport and Dispersion of Rafting Vegetation in the Sacramento-San Joaquin Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The research we are proposing here is focused on developing a thorough, mechanistic understanding of how rafting vegetation, such as hyacinths or egeria, is transported in the Sacramento-San Joaquin Delta. Our approach is to examine in detail the forces that act on rafts of vegetation, and the resulting raft accelerations, to establish a predictive model of raft pathlines. Our model development will be built around a series of field experiments that include measurements of raft movement using GPS-logging drifters integrated into rafts, tidal and wind-forcing using a boat mounted current profiler and an anemometer, and direct estimation of the water-induced shear stress using a point velocity meter incorporated into the actual rafts. These field observations will be used to critically evaluate a numerical model of both channel (tidal) flows and resulting raft movement. Our initial development will include a highly-resolved channel flow model, which will explicitly capture more lateral variability, including low velocity side “pockets”, than is typically resolved with Delta scale hydrodynamic models. Initially, this will allow us to carefully evaluate the quality of our raft tracking calculations. Once the approach is established to be accurate, however, these high-resolution flows will be used to numerically calculate the effective advection and dispersion of rafts in the Delta channel under consideration. This analysis will be focused on parameterizing the effects on raft transport of structures and processes that are unresolved in typical Delta hydrodynamics models. An example of a process that is likely to be important to parameterize is the trapping and retention of rafts along the perimeter of channels due to off-axis wind forcing, and the resulting along-channel dispersion of rafts. In order to examine the effective advection and dispersion of rafts in Delta channels, we propose to pursue this combination of field and numerical studies of raft transport in locations of increasing complexity: first in idealized, straight channels, then in a natural, sinuous channel and a channel junction, and finally throughout the entire Delta. Our research is strongly motivated by the desire to provide a predictive model of dispersion in the Delta for floating objects that respond to both wind and tidal forcing. Immediate applications involve the movement of hyacinth rafts and egeria to evaluate potential management strategies. Important future applications are likely to include consideration of other biological invasions, due to the potential for rafts to provide a transport pathway, and analysis of the movement of accidental or intentional releases of floating material in the Delta.
    Science topics None specified
    Updated November 29, 2022
  • Title

    A Calibration-Free Approach to Modeling Delta Flows and Transport

    Lead University of California - Berkeley [UC Berkeley]
    Description The purpose of this project is to develop and evaluate an integrated system for the prediction of Delta flows and transport in real-time that doesn't rely upon historical data sets for calibration and validation. The system consists of observational and computational components, along with real-time communication and coordination.
    Science topics None specified
    Updated April 29, 2022
  • Title

    Impact of Urbanization on Chinook Salmon, Steelhead Trout, and Their Prey: a Case Study of the American River

    Lead University of California - Berkeley [UC Berkeley]
    Description The American River provides spawning/rearing habitat for Chinook salmon and steelhead, yet passes through 30 miles of dense urban development. Urban runoff contains pyrethroid insecticides that cause the river to become toxic to standard testing species with every storm event. This study will go beyond observed toxicity, and address toxicity to chironomids, caddisflies, and mayflies, key diet components of juvenile fish in the river. A bioenergetic model will be used to evaluate effects of food web changes on young salmonids. Our key approach is the use of river-side systems with flowing river water that allow us to replicate realistic pesticide exposures, while controlling other variables. We will determine sensitivity to pyrethroids and fipronil of salmonid prey taxa, and expose them, as well as standard testing species, in the flow-through systems through six storm events. We will maintain experimental streams containing riverine benthic invertebrate communities, and measure response to the pyrethroid pulses. To supplement analyses of the indirect, food web-mediated effects, we will measure endocrine effects through vitellogenin induction in salmon and steelhead. Finally, one treatment includes river water from which organic contaminants have been removed by activated charcoal, to help establish cause of toxicity. The goal is to determine if known toxicity in the American River is a threat to benthic invertebrates and, through the food web, to salmon and steelhead.
    Science topics Chinook Salmon, Steelhead Trout, Above highwater refugia, Other discharge contaminants, Food webs
    Updated April 29, 2022
  • Title

    Estuarine fish community responses to climate, flow, and habitat

    Lead University of California - Berkeley [UC Berkeley]
    Description

    The goal of this research is to better understand how climate change will affect fishes with different life histories and habitat associations across the San Francisco Estuary. Existing datasets will be incorporated in synthetic analyses and cutting-edge statistical models to identify fish community responses to climate, flows, and habitats along the estuarine salinity gradient. This synthesis-science project will use rich long-term datasets that have been collected by Bay-Delta researchers for decades that will then be analyzed in a reproducible and open science framework. It will also support efforts by the Interagency Ecological Program’s Climate Change Project Work Team.
    Science topics Estuaries
    Updated February 27, 2025
  • Title

    Identification of environmental conditions driving cyanobacterial multi-species blooms and their toxicity using genome resolved metagenomics

    Lead University of California - Berkeley [UC Berkeley]
    Description In recent years the Sacramento-San Joaquin Delta has seen an increase in toxigenic cyanobacterial diversity and abundance during harmful cyanobacterial bloom events (cyanoHABs). This increased cyanobacterial diversity parallels an increase in the number of detected toxins during cyanoHABs outside of the typical microcystins that have been previously identified. Currently there are critical knowledge gaps around the full toxigenic potential of rising diversity of cyanobacterial species, and how the total microbial community of cyanoHABs interacts within itself and with external abiotic factors in ways that may promote the expansion of new and diverse cyanoHABs. The goal of this study is to use genome-resolved metagenomics to study the genetic diversity and metabolic and toxigenic potential of cyanoHABs to i) identify cyanobacterial taxa composition and their potential for toxins biosynthesis ii) characterize species succession dynamics and metabolic processes of the full microbial community during cyanobacterial bloom phases, iii) correlate environmental factors and toxin titers with biological components of diverse bloom phases to explain the development of cyanobacterial multi-species dominated bloom.
    Science topics Cyanobacteria, Harmful algal blooms HAB
    Updated February 27, 2025
  • Title

    Restoring tidal marsh foodwebs: assessing restoration effects on trophic interactions and energy flows in the San Francisco Bay-Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The objective of this research on tidal marsh food webs is to examine whether and how restoration (via breaching dikes) may translate into recovery of diverse energy pathways and trophic interactions between basal resources, primary consumers, and predators. By comparing food webs at several tidal marshes, I will answer the following questions: (1) How does food web structure vary between reference and restored tidal marshes over time (seasons and years) and across a salinity gradient? (2)What mechanisms explain variation in food web structure within and between reference and restored tidal marshes–are they related to energy flows (food quantity, quality, transfer efficiency), community composition, or both? (3) What role do non-native species play in potentially shifting food web structure–e.g., changing community membership, sequestering energy from natives? This project builds on a large breadth of research that has used stable isotopes to characterize tidal marsh food webs in the Bay-Delta and other regions.
    Science topics Food webs, Wetlands
    Updated February 27, 2025
  • Title

    Examining the relationship between Longfin Smelt and flow in the San Francisco Bay Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The number of longfin smelt in the San Francisco Estuary has been in decline for the past several decades. While decreased freshwater flow reaching the estuary has been identified as a contributing factor, the relationship between flow and smelt populations has proven complex and appears to be changing over time. This study examined how water flow affects longfin smelt populations across different habitats in the San Francisco Estuary, analyzing decades of monitoring data from state and federal agencies. The research explored both where smelt live in the estuary and how their populations change over time in response to varying water flows. The findings show that more freshwater flow generally helps smelt populations, especially young fish in shallow waters. However, this beneficial effect appears to be weakening over time in some areas, particularly in open waters away from the shore. This suggests that smelt may be adapting to changing conditions by moving to different parts of the estuary. To help protect this threatened species, conservation efforts may need to focus on both restoring natural water flows and improving habitat conditions throughout the estuary.
    Science topics Fish, Flows, Longfin Smelt, Zooplankton
    Updated February 27, 2025
  • Title

    Carbon Biogeochemical Cycling in Tidal Wetlands: Exploring Lateral Carbon Exchange and Sequestration Potential

    Lead University of California - Berkeley [UC Berkeley]
    Description Tidal wetlands, at the interface of land and ocean, play a critical role in carbon biogeochemical cycling and have the potential to provide major feedback to the Earth system through greenhouse gas exchange and long-term carbon sequestration. However, the efficiency of carbon sequestration in tidal systems relies on both vertical carbon exchange with the atmosphere and lateral tidal exchange with adjacent water bodies. Unfortunately, the importance of hydrologic carbon fluxes has been largely overlooked, leaving a crucial aspect of coastal wetland net carbon balance unaddressed. We employed an integrated approach to quantify vertical and lateral carbon exchange and studied their dynamics, combining eddy covariance flux measurements with on-site water quality and tidal discharge measurements, as well as manual 24h surface water samplings. Our measurements were conducted in a recently restored tidal freshwater marsh in the Sacramento-San Joaquin Delta, CA, that stands out in global networks like FLUXNET and Ameriflux owing to its impressive net ecosystem exchange of -850 g C m-2 yr-1. Using wavelet decomposition, we examined the variability of carbon exchange (CO2 and CH4) across different timescales. Through information theory and mutual information analysis, we assessed the factors influencing both vertical and lateral exchanges. Our preliminary findings suggest that variability in carbon exchange is largest at the diel scale, with plant gross primary productivity and tidal fluctuations in depth having the most significant interactions with CO2 and CH4 fluxes, respectively. Furthermore, our tidal cycle samplings revealed that dissolved inorganic carbon dominates the fraction of lateral carbon loss, accounting for approximately 80% of the export. Remarkably, similarities existed between the values for net lateral carbon export and ecosystem respiration, signifying that the dissolved, terrestrial-to-ocean carbon flux could represent one of the primary fates of the fixed carbon in this tidal ecosystem. These large dissolved inorganic carbon fluxes and their chemical speciation, are important to consider when estimating the climate mitigation potential of restored tidal wetlands.
    Science topics Carbon, Carbon storage, Greenhouse gas GHG
    Updated January 30, 2024
  • Title

    Pixel-Wise Footprint Analysis of GPP Using High-Resolution NDVI/NIRv Data

    Lead University of California - Berkeley [UC Berkeley]
    Description Spectral indices such as NDVI have long been found to be good predictors of plant productivity at many spatial scales from the canopy to the landscape. Spectral indices are an important tool for upscaling GPP fluxes we measure at the ecosystem scale through Eddy Covariance up to larger spatial scales. Other indices, such as NIRv (expressed as NDVI * total NIR) have also been shown to be potentially more accurate predictors of GPP using in-situ spectral measurements than NDVI alone. Additionally, associating spectral signals within modeled flux footprint areas has been shown to improve the predictive capability of spectral indices compared to estimates using remotely sensed data centered directly on top of flux towers. Most if not all of these spatially explicit footprint analyses have been done by aggregating footprints into polygons based on their 50%-90% estimated flux contributions, and then associating those polygons with fluxes and spectral signals within them. This approach has been necessary largely because of the spatial scales involved with satellite remote sensing products, reaching a practical minimum of 3m, downsampled from 4.8m imagery by Planet Labs. By combining pixel-weighted flux footprint contributions with ultra-high resolution (3cm) spectral drone data, we will examine and compare how different spatial scales and indices affect the capability of spectral data to predict fluxes which are not directly measured.
    Science topics None specified
    Updated January 30, 2024
  • Title

    Monitoring Sacramento River winter-run Chinook salmon life history diversity, growth, and habitat use among varying hydroclimatic regimes

    Lead University of California - Berkeley [UC Berkeley]
    Description Sacramento River winter-run Chinook salmon have been endangered since 1994. Historically, the fish spawned during summer in cool tributaries upstream of Sacramento, but dams have limited spawning habitat to a small reach of the river. Today, survival of their offspring is heavily dependent on cool summer water releases from reservoirs, which also provide critical water supplies for irrigation, municipal, and industrial needs, as well as providing flood control and hydropower generation. During drought, this can lead to difficult management decisions. Understanding how winter run Chinook salmon respond to drought and water temperature is therefore vital to the management of this endangered population. This project tackled two outstanding questions about winter-run salmon ecology. The first was how winter-run Chinook use different rearing habitats during drought and non-drought periods, and the second was to explore which habitats provide enhanced growth during drought and non-drought periods. To answer these questions, UC Berkeley post-doc Pedro Morais used isotopic analysis of otoliths, or fish ear bones, which grow continuously throughout their lives and therefore carry a record of their environment and growth. Using otoliths, researchers can reconstruct details of fishes’ lives, including water temperature and migration patterns.
    Science topics None specified
    Updated February 1, 2024
  • Title

    Advancing a collaboratory for equitable stewardship of the Sacramento-San Joaquin River Delta watershed

    Lead University of California - Berkeley [UC Berkeley]
    Description

    Decisions over how water is allocated consider a limited range of climate and operational scenarios, privilege Western knowledge, and are generally inaccessible to the public, including communities most affected by water decision-making. We will follow a participatory and iterative co-production process to understand and integrate the diverse values and uses of Delta waterways and floodplains in an accessible knowledge platform designed to promote public engagement, learning, and equitable stewardship.

    The overarching goal of the proposed project is to build and integrate knowledge of the social-ecological uses of Delta waterways and floodplains to inform equitable solutions to Delta management challenges. Specific objectives are to (1) understand the diverse public beneficial uses Delta waterways and floodplains; (2) incorporate functional flows and riparian floodplain processes in Delta water operations models; (3) share diverse community knowledge through a web-based platform; and (4) critically evaluate our collaborative research approach to assess its efficacy in building trust, enhancing public engagement, and guiding equitable stewardship actions. 
    Science topics None specified
    Updated July 16, 2025