Science activities

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.

This study focuses on understanding how restored tidal wetlands with different physical configurations function as refuge and rearing habitat for fishes, including native and imperiled species such as delta smelt and juvenile Chinook salmon. This research will assess the spatial distribution of predation risk as it varies within and across tidal wetlands. The proposed research will generate a statistical model that helps predict predation outcomes from various restored tidal wetland designs and channel configurations. This will be a powerful tool for managers to forecast how proposed habitat restoration or water management actions may impact native fish populations.

Pesticide and nutrient inputs from human activities are present in the Sacramenot-San Joaquin Bay-Delta, but the impact of these stressors together on algae is not well known. This research will examine the impacts of herbicides and nutrients on the growth and stress responses of phytoplankton and cyanobacteria present in the San Francisco Estuary. The algae in the delta are diverse with critical ecological effects, ranging from toxin-producing cyanobacteria that form hazardous algal blooms to benthic diatoms and green algae that make up the bulk of the aquatic food web. Contaminants and herbicides can cause changes in algae cellular health which may impact population growth. Understanding algal sub-lethal stress responses will improve our understanding of stressors on the bay-delta food web and bloom formation.

This project aims to improve understanding of atmospheric and hydrologic carbon fluxes in a restored tidal salt marsh in the South San Francisco Bay. I will use soil chambers to measure how much carbon dioxide and methane is taken in and emitted from the marsh. The project will also examine how spatial variability in marsh surface cover impact these exchanges. Shahan will use the data collected in this study to create a biogeochemical model that estimates the carbon budgets of wetlands in the Bay-Delta. A complete carbon budget will illuminate relationships between carbon fluxes and environmental variables. This information can support more informed management of wetlands, as well as allow researchers and decision makers to more effectively plan wetland restoration to be effective in managing carbon fluxes in the face of possible impacts due to climate change.

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.

This project aims to characterize and quantify where detrital material (decaying plant matter) originates within wetlands, the composition of that material, and how export of detrital particles occurs. This project will combine powerful characterization tools and techniques that scale from molecules to ecosystems to assess spatial and temporal trends in particle sources, species and composition. Because restoration in the Sacramento-San Joaquin Delta will fundamentally alter particle distribution and food availability for aquatic organisms, this study will inform habitat restoration efforts and the revival of native fish populations. The tools developed and adapted for this project may inform management response during extreme conditions and climate events by helping to identify areas that may act as refugia for species.

This study will investigate fish swim performance in response to temperature, using salmon and two of its known predators: largemouth bass and Sacramento pikeminnow. The researcher will assess swim performance metrics and predation risk inside and outside the ideal thermal range of each species to determine if a temperature advantage predicts salmon survival in predation scenarios. This project’s results will provide a mechanistic understanding of how temperature stress may influence mortality risk of juvenile Chinook salmon through predation, which will offer a more holistic perspective on the management of this species

This project work will model the risk of pesticide pollution in 225 sub-catchments of the Sacramento-San Joaquin Bay-Delta. The model will account for water management practices, land use, pesticide use rates, and cumulative pesticide stress. Additionally, this work will produce a web-based tool to simulate current and future risks based on the ranking of primary sources of pesticide contribution. This work will provide a framework to predict risk from chemical stressors. Specific objectives are: (1) enhanced pro-active chemical risk assessment, (2) creation of a tool which enables science-based chemical use decisions, (3) improved risk screening for vulnerable areas, and (4) identification of adverse effects of current and future chemical use strategies.

This project focuses on nitrogen and carbon cycling within the Bay-Delta, both before and after planned 2021 upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP). We will measure in situ benthic nitrate (NO3- ) and oxygen (O2) fluxes using a new non-invasive technique, which provides high frequency continuous data over a much larger sediment surface area than traditional methods. The SRTWP currently represents one of the largest point sources of nitrogen to the Bay-Delta, with the upgrades projected to cut nitrogen outputs from the plant by ~65%. This project will help assess the efficacy of this major management action and our results will add to biogeochemical models for the Bay-Delta.