Science activities

AmeriFlux is a network of PI-managed sites measuring ecosystem CO2, water, and energy fluxes in North, Central and South America. AmeriFlux is now one of the DOE Office of Biological and Environmental Research (BER) best-known and most highly regarded brands in climate and ecological research. AmeriFlux datasets, and the understanding derived from them, provide crucial linkages between terrestrial ecosystem processes and climate-relevant responses at landscape, regional, and continental scales. Scientific Questions What are the magnitudes of carbon storage and the exchanges of energy, CO2 and water vapor in terrestrial systems? What is the spatial and temporal variability? How is this variability influenced by vegetation type, phenology, changes in land use, management, and disturbance history, and what is the relative effect of these factors? What is the causal link between climate and the exchanges of energy, CO2 and water vapor for major vegetation types, and how does seasonal and inter-annual climate variability and anomalies influence fluxes? What is the spatial and temporal variation of boundary layer CO2 concentrations, and how does this vary with topography, climatic zone and vegetation?

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.

SacPAS serves to provide information integration services to the Central Valley Project Improvement Act and practitioners working on matters related to ESA-listed fishes. The web-based services relate fish passage to environmental conditions and provide resources for evaluating the effects of river management and environmental conditions on salmon passage and survival.

The work performed as part of this agreement includes developing, maintaining, and making accessible query tools and decision support tools to access: historical, real-time and forecasted data; data summaries and visualizations; and hindcasts, forecasts, and scenario-derived predictions from statistical and mechanistic models. More specifically, the objectives are to: 

1)    Maintain and extend a secondary data repository of historical, real-time, and forecasted fish, environmental, and operational data from the Sacramento River and other river systems in the Central Valley, integrated from primary, public databases. 

2)    Maintain and improve the data query and visualization tools and services provided through the SacPAS website (https://www.cbr.washington.edu/sacramento/) for historical, real-time, and forecasted environmental and fish data.

3)    Conduct research and provide access to modeling tools for fish survival and migration, through the SacPAS website, in support of Reclamation-funded and ESA-mandated activities, especially in efforts to predict, track, and evaluate the efficacy of proposed or actual actions.
 

Chinook Salmon (Oncorhynchus tshawytscha) populations in California are in decline due to the combined effects of habitat degradation, water diversions, and shifting climate regimes. This project uses archival tissues (otoliths, vertebrae) from modern and ancient spring-run Chinook Salmon to understand how shifts in migration timing and habitat use allowed salmon to cope with highly variable environmental conditions. We will learn how salmon responded to the recent drought and flood periods (2012-2020 CE), the California Gold Rush Period (~1835-1870 CE), the Little Ice Age (~1560-1780 CE), and the Megadrought Period (~1200-1410 CE). This effort will provide the insights needed for developing climate-adapted conservation actions to support salmon into the future.

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.