The Biogeochemistry (BGC) Group uses an interdisciplinary approach to address surface water quality issues and food web dynamics throughout California, particularly in the Sacramento-San Joaquin Delta and San Francisco Bay.
Study areas include:
- Drivers of phytoplankton community composition and abundance and harmful algal bloom-related toxins
- Long-term continuous monitoring of numerous water quality constituents, phytoplankton, phytoplankton community structure, dissolved organic carbon and nitrogen as well as other constituents important to aquatic systems
- Changes in wastewater-derived nutrients and effects on phytoplankton community structure
- Effects of flow and water residence time on nutrient cycling and phytoplankton
- The impacts of invasive aquatic vegetation on water quality, water residence time, and native phytoplankton
- Assessing the role of wetlands in the Delta with respect to such topics as mercury, nutrients, drinking water quality and phytoplankton production
- Assessing the potential of tidal wetlands to mitigate land subsidence and sequester carbon
- Supporting improved water quality management through development of new sensors, analyses and techniques such as direct residence time measurements, custom sensor technologies, wide-area high-speed mapping surveys, remote sensing calibration and validation and other related activities
The BGC Group specializes in the application of in-situ optical sensors that monitor short- and long-term water quality trends. These sensors measure a host of biogeochemical parameters and capture continuous temporal trends – including those that may go undetected through traditional discrete sampling. The BGC Group also employs novel high-resolution boat-based mapping surveys, conducting intensive sampling for a diverse variety of biogeochemical parameters throughout the Bay-Delta.
These studies and data will help resource managers assess response to management actions and predict how the Bay-Delta will respond to future changes. The high frequency, real-time data can act as an early warning system for unanticipated, short-lived, or rapidly changing conditions, such as those due to spills, harmful algal blooms, and altered water-quality resulting from storms or levee breaches. The BGC group additionally specialize in the creation of novel data dissemination techniques in effort to ease open data acquisition, ultimately aiming to advance Bay-Delta science.
Additional Biogeochemistry Group staff include:
- Malanyon Adams
- Dulci Avouris
- Tom Bergamaschi
- Tim Baxter
- Heidi Bockisch
- Bryan Bonham
- Jake Brinkman
- Dylan Burau
- Jordy Conneely
- Ayelet Delascagigas
- Patrick Dellwo
- Nicholas Framsted
- Tommy (Hieu) Ly
- Andrea Jaegge
- Nathan Jumps
- Colin Keating
- Anne Le
- Ariana Maestas
- Kat Mai Cone
- Schuyler Nardelli
- Erica Nejad
- Dianna Oros
- Emily Richardson
- Tara Schraga
- Jesse Schroeder
- Jennifer Soto-Perez
- Corrine Sanford
- Crystal Sturgeon
- Maura Uebner
Below are other science projects associated with this project.
Assessing Sediment Nutrient Storage and Release in California's Sacramento-San Joaquin Delta
Evaluating the effects of wastewater-derived nutrients on phytoplankton abundance and community structure in the San Francisco Estuary and Delta
Modeling Nitrogen Reduction Benefit to Invasive Aquatic Vegetation vs. Native Phytoplankton
Monitoring Cyanotoxins in California's Sacramento-San Joaquin Delta: Fixed Stations and High-Resolution Mapping Surveys
Creating a Model to Predict Future Carbon Levels in Tidally-driven Marshes
Trends in Dissolved Organic Carbon (DOC) in the Sacramento-San Joaquin Delta
Methylmercury and Low Dissolved Oxygen Events in Suisun Marsh
Mercury and Dissolved Organic Matter in Delta Wetlands
Sources of Disinfection Byproduct-forming Material in the State Water Project
High-Speed Mapping of Nutrient Distributions and Water Quality Survey - Lower South San Francisco Bay
Dynamics of zooplankton in the Cache Slough Complex
Phytoplankton production and nutrient transformations in shallow water wetland habitats
Below are publications associated with this project.
Lateral carbon exports from drained peatlands: An understudied carbon pathway in the Sacramento-San Joaquin Delta, California
Tidal wetland gross primary production across the continental United States, 2000–2019
Spatial variability of phytoplankton in a shallow tidal freshwater system reveals complex controls on abundance and community structure
Chemically enhanced treatment wetland to improve water quality and mitigate land subsidence in the Sacramento-San Joaquin Delta: Cost and design considerations
Sequestration and transformation in chemically enhanced treatment wetlands: DOC, DBPPs and Nutrients
Aluminum- and iron-based coagulation for in-situ removal of dissolved organic carbon, disinfection byproducts, mercury and other constituents from agricultural drain water
Effects of ferric sulfate and polyaluminum chloride coagulation enhanced treatment wetlands on Typha growth, soil and water chemistry
Procedures for using the Horiba Scientific Aqualog® fluorometer to measure absorbance and fluorescence from dissolved organic matter
Sediment accretion and carbon storage in constructed wetlands receiving water treated with metal-based coagulants
Wetlands receiving water treated with coagulants improve water quality by removing dissolved organic carbon and disinfection byproduct precursors
Direct and indirect effects of tides on ecosystem-scale CO2 exchange in a brackish tidal marsh in Northern California
Use of flow cytometry and stable isotope analysis to determine phytoplankton uptake of wastewater derived ammonium in a nutrient-rich river
Below are data or web applications associated with this project.
Bay-Delta Water Quality Survey, 2018 and 2020 Comparison
Delta Survey Data Visualization Contents for 2018 and 2020
Bay- Delta Water Quality, Nutrient and Phytoplankton Mapping | US Geological Survey
Data visualization tool created for California's Bay-Delta Regional Monitoring Program. This web applicaton visualizes nutrients and phytoplankton spatially and temporally.
Assessing Phytoplankton and Nutrient Abundance in the San Francisco Estuary and Delta
A data visualizatoin exploring the relationship between nutrient distribution and phytoplankton under different conditions across the San Francisco Delta and Estuary. Assessing distribution and abundance aids understanding of how managing nutrient supplies affects aquatic food webs, helping managers evaluate the potential environmental benefits of future nutrient reduction efforts agains
Below are news stories associated with this project.
Below are partners associated with this project.
- Overview
The Biogeochemistry (BGC) Group uses an interdisciplinary approach to address surface water quality issues and food web dynamics throughout California, particularly in the Sacramento-San Joaquin Delta and San Francisco Bay.
Study areas include:
- Drivers of phytoplankton community composition and abundance and harmful algal bloom-related toxins
- Long-term continuous monitoring of numerous water quality constituents, phytoplankton, phytoplankton community structure, dissolved organic carbon and nitrogen as well as other constituents important to aquatic systems
- Changes in wastewater-derived nutrients and effects on phytoplankton community structure
- Effects of flow and water residence time on nutrient cycling and phytoplankton
- The impacts of invasive aquatic vegetation on water quality, water residence time, and native phytoplankton
- Assessing the role of wetlands in the Delta with respect to such topics as mercury, nutrients, drinking water quality and phytoplankton production
- Assessing the potential of tidal wetlands to mitigate land subsidence and sequester carbon
- Supporting improved water quality management through development of new sensors, analyses and techniques such as direct residence time measurements, custom sensor technologies, wide-area high-speed mapping surveys, remote sensing calibration and validation and other related activities
Biogeochemistry group scientists collect water quality data on the Sacramento-San Joaquin Delta The BGC Group specializes in the application of in-situ optical sensors that monitor short- and long-term water quality trends. These sensors measure a host of biogeochemical parameters and capture continuous temporal trends – including those that may go undetected through traditional discrete sampling. The BGC Group also employs novel high-resolution boat-based mapping surveys, conducting intensive sampling for a diverse variety of biogeochemical parameters throughout the Bay-Delta.
These studies and data will help resource managers assess response to management actions and predict how the Bay-Delta will respond to future changes. The high frequency, real-time data can act as an early warning system for unanticipated, short-lived, or rapidly changing conditions, such as those due to spills, harmful algal blooms, and altered water-quality resulting from storms or levee breaches. The BGC group additionally specialize in the creation of novel data dissemination techniques in effort to ease open data acquisition, ultimately aiming to advance Bay-Delta science.
Additional Biogeochemistry Group staff include:
- Malanyon Adams
- Dulci Avouris
- Tom Bergamaschi
- Tim Baxter
- Heidi Bockisch
- Bryan Bonham
- Jake Brinkman
- Dylan Burau
- Jordy Conneely
- Ayelet Delascagigas
- Patrick Dellwo
- Nicholas Framsted
- Tommy (Hieu) Ly
- Andrea Jaegge
- Nathan Jumps
- Colin Keating
- Anne Le
- Ariana Maestas
- Kat Mai Cone
- Schuyler Nardelli
- Erica Nejad
- Dianna Oros
- Emily Richardson
- Tara Schraga
- Jesse Schroeder
- Jennifer Soto-Perez
- Corrine Sanford
- Crystal Sturgeon
- Maura Uebner
- Science
Below are other science projects associated with this project.
Filter Total Items: 18Assessing Sediment Nutrient Storage and Release in California's Sacramento-San Joaquin Delta
Sediments represent an important pool of nutrients in the Sacramento-San Joaquin Delta (Delta). The exchange of nutrients between the water column and the benthos impacts water quality and effects phytoplankton, harmful algal blooms, aquatic vegetation, and drinking water quality. To date, there is very limited information about nutrient pools in Delta sediments, nor how these nutrients are...Evaluating the effects of wastewater-derived nutrients on phytoplankton abundance and community structure in the San Francisco Estuary and Delta
Planned upgrades to the Sacramento Regional wastewater treatment plant (SRWTP) will substantially reduce nutrient discharge and also alter the types and amounts of nutrients being distributed across the San Francisco Delta and Estuary (Delta). One highly anticipated outcome of lower nutrients is improved productivity in the phytoplankton communities that supply aquatic food webs, which should...Modeling Nitrogen Reduction Benefit to Invasive Aquatic Vegetation vs. Native Phytoplankton
Phytoplankton comprise the bottom of the aquatic food web and the abundance of phytoplankton serves as an indicator of healthy aquatic habitats. In the Sacramento-San Joaquin River Delta (Delta), competing with phytoplankton for required nitrogen, invasive aquatic vegetation (IAV) has increased exponentially in recent years. Once established, IAV can negatively impact local ecosystems and...Monitoring Cyanotoxins in California's Sacramento-San Joaquin Delta: Fixed Stations and High-Resolution Mapping Surveys
California’s Sacramento-San Joaquin River Delta (Delta) provides drinking water to about 30 million people and irrigation water to the agriculturally rich Central Valley. The Delta is also home to numerous threatened and endangered native species. The health of the Delta's aquatic ecosystems, and fish in particular, have long been in a state of decline. This is associated with decreasing...Creating a Model to Predict Future Carbon Levels in Tidally-driven Marshes
Tidal marshes are important ecosystems in the San Francisco-Bay Delta. They remove carbon from the atmosphere, they build up soils that buffer our communities from sea level rise, they provide critical habitat and food resources for a diversity of species, and they reduce excessive nutrients which have a negative impact on water quality. As a result of land-use change and urbanization, the San...Trends in Dissolved Organic Carbon (DOC) in the Sacramento-San Joaquin Delta
Water from the Sacramento-San Joaquin Delta contains high concentrations of disinfection byproduct-forming (DBP-forming) materials when treated for potable use. DBPs form when dissolved organic compounds (DOC) in water react with disinfectants such as chlorine and ozone during the water treatment process. The amount of DBPs that form is a function of both the amount and source of the DOC, both of...Methylmercury and Low Dissolved Oxygen Events in Suisun Marsh
The primary purpose of the USGS portion of this proposed study is to evaluate if spectrophotometric and spectrofluorometric methods are useful for identifying organic sources of oxygen demand by analyzing water-quality samples (DO, BOD, Chl, SSC, Salinity, THg, MeHg) collected by other agencies and project participants. Sources to be evaluated include algal production, vegetation, soils, and...Mercury and Dissolved Organic Matter in Delta Wetlands
Between 1860 and 1914, hydraulic mining activities sent more than 800,000,000 cubic yards of mercury-laden sediment into the Delta altering the landscape, water flows, and contributing to the leveeing and reclamation of the Delta's marshes. Transport of mercury from historic mining areas continues today. The sedimentary supply of mercury to the Delta and in Delta sediments (cinnabar, metacinnabar...Sources of Disinfection Byproduct-forming Material in the State Water Project
Water from the Sacramento-San Joaquin Delta contains high concentrations of disinfection byproduct-forming (DBP-forming) materials when treated for potable use. DBPs form when dissolved organic compounds (DOC) in water react with disinfectants such as chlorine and ozone during the water-treatment process. The amount of DBPs that form is a function of the amount and source of the DOC, both of which...High-Speed Mapping of Nutrient Distributions and Water Quality Survey - Lower South San Francisco Bay
This project aims to characterize spatial heterogeneity for key water quality parameters, and pilot the use of underway-flowthrough mapping of biogeochemical properties as a cost-effective approach to monitoring.Dynamics of zooplankton in the Cache Slough Complex
Our purpose is to investigate what controls the distribution and abundance of fish prey within the Cache Slough Complex (CSC).Phytoplankton production and nutrient transformations in shallow water wetland habitats
The objectives of this study are to quantify and characterize (1) phytoplankton production on Liberty Island, (2) utilization and transformation of nutrients, and (3) attenuation/loss of phytoplankton as the material is transported from Liberty Iisland into Cache Slough. - Multimedia
- Publications
Below are publications associated with this project.
Filter Total Items: 69Lateral carbon exports from drained peatlands: An understudied carbon pathway in the Sacramento-San Joaquin Delta, California
Degradation of peatlands via drainage is increasing globally and destabilizing peat carbon (C) stores. The effects of drainage on the timing and magnitude of lateral C losses from degraded peatlands remains understudied. We measured spatial and temporal variability in lateral C exports from three drained peat islands in the Sacramento‐San Joaquin Delta in California across the 2017 and 2018 waterAuthorsChristina M. Richardson, Joseph K. Fackrell, Tamara E. C. Kraus, Megan B. Young, Adina PaytanTidal wetland gross primary production across the continental United States, 2000–2019
We mapped tidal wetland gross primary production (GPP) with unprecedented detail for multiple wetland types across the continental United States (CONUS) at 16‐day intervals for the years 2000–2019. To accomplish this task, we developed the spatially explicit Blue Carbon (BC) model, which combined tidal wetland cover and field‐based eddy covariance tower data into a single Bayesian framework, and uAuthorsR.A. Feagin, I. Forbrich, T. P. Huff, J.G. Barr, J. Ruiz-Plancarte, J.D. Fuentes, R.G. Najjar, R. Vargas, A. Vazquez Lule, L. Windham-Myers, Kevin D. Kroeger, E. J. Ward, G. W. Moore, M. Leclerc, K. W. Krauss, C.L. Stagg, M. Alber, S. H. Knox, K. V. R. Schafer, T.S. Bianchi, J. A. Hutchings, H. Nahrawi, A. Noormets, B. Mitra, A. Jaimes, A.L. Hinson, Brian A. Bergamaschi, J.S. King, G. MiaoSpatial variability of phytoplankton in a shallow tidal freshwater system reveals complex controls on abundance and community structure
Estuaries worldwide are undergoing changes to patterns of aquatic productivity because of human activities that alter flow, impact sediment delivery and thus the light field, and contribute nutrients and contaminants like pesticides and metals. These changes can influence phytoplankton communities, which in turn can alter estuarine food webs. We used multiple approaches-including high-resolution wAuthorsElizabeth Stumpner, Brian A. Bergamaschi, Tamara E. C. Kraus, Alexander Parker, Francis Wilkerson, Bryan D. Downing, Richard Dugdale, Michael T. Murrell, Kurt D. Carpenter, James Orlando, Carol KendallChemically enhanced treatment wetland to improve water quality and mitigate land subsidence in the Sacramento-San Joaquin Delta: Cost and design considerations
Water quality impairment and land surface subsidence threaten the viability of the Sacramento-San Joaquin Delta (Delta), a critical component of California’s water conveyance system. Current day irrigation drainage through Delta island peat soils impacts drinking water treatment and is linked to mercury transport, potentially posing both ecological and public health concerns. Hybrid coagulation-trAuthorsPhilip A. M. Bachand, Tamara E. C. Kraus, William R. Horwath, Nathan R. Hatch, Sandra M. BachandSequestration and transformation in chemically enhanced treatment wetlands: DOC, DBPPs and Nutrients
We examined the effectiveness of chemically enhanced treatment wetlands (CETWs), wetlands that received water treated with coagulants, to remove dissolved organic carbon (DOC), disinfection byproduct precursors (DBPPs), nutrients and metals from agricultural drain water. Wetlands consisted of controls with no coagulant addition, ferric sulfate dosed and polyaluminum chloride dosed treatments. CETWAuthorsPhilip A. M. Bachand, Sandra M. Bachand, Tamara E. C. Kraus, Dylan Stern, Yan Ling Liang, William R. HorwathAluminum- and iron-based coagulation for in-situ removal of dissolved organic carbon, disinfection byproducts, mercury and other constituents from agricultural drain water
Agricultural production on wetland soils can be significant sources of dissolved organic carbon (DOC), disinfection byproduct precursors, mercury and nutrients to downstream water bodies and accelerate land subsidence. Presented as a potential solution for in-situ water quality improvement and land subsidence mitigation, chemically enhanced treatment wetlands (CETWs) were used to leverage both coaAuthorsSandra M. Bachand, Tamara E. C. Kraus, Dylan Stern, Yan Ling Liang, William R. Horwath, Philip A. M. BachandEffects of ferric sulfate and polyaluminum chloride coagulation enhanced treatment wetlands on Typha growth, soil and water chemistry
Land surface subsidence is a concern in many deltas worldwide as it contributes to water quality degradation, loss of fertile land and increased potential for levee failure. As a possible solution to these concerns, on-site coagulation enhanced treatment wetlands(CETWs), coagulation water treatment followed by wetland passage serving as a settling basin, were implemented in a field-scale study locAuthorsYan Ling Liang, Tamara E. C. Kraus, Lucas C. R. Silva, Philip A. M. Bachand, Sandra M. Bachand, Timothy A. Doane, William R. HorwathProcedures for using the Horiba Scientific Aqualog® fluorometer to measure absorbance and fluorescence from dissolved organic matter
Advances in spectroscopic techniques have led to an increase in the use of optical measurements (absorbance and fluorescence) to assess dissolved organic matter composition and infer sources and processing. Although optical measurements are easy to make, they can be affected by many variables rendering them less comparable, including by inconsistencies in sample collection (for example, filter porAuthorsAngela M. Hansen, Jacob Fleck, Tamara E. C. Kraus, Bryan D. Downing, Travis von Dessonneck, Brian A. BergamaschiSediment accretion and carbon storage in constructed wetlands receiving water treated with metal-based coagulants
In many regions of the world, subsidence of organic rich soils threatens levee stability and freshwater supply, and continued oxidative loss of organic matter contributes to greenhouse gas production. To counter subsidence in the Sacramento-San Joaquin Delta of northern California, we examined the feasibility of using constructed wetlands receiving drainage water treated with metal-based coagulantAuthorsElizabeth Stumpner, Tamara E. C. Kraus, Yan Liang, Sandra M. Bachand, William R. Horwath, Philip A.M. BachandWetlands receiving water treated with coagulants improve water quality by removing dissolved organic carbon and disinfection byproduct precursors
Constructed wetlands are used worldwide to improve water quality while also providing critical wetland habitat. However, wetlands have the potential to negatively impact drinking water quality by exporting dissolved organic carbon (DOC) that upon disinfection can form disinfection byproducts (DBPs) like trihalomethanes (THMs) and haloacetic acids (HAAs). We used a replicated field-scale study locaAuthorsAngela M. Hansen, Tamara E. C. Kraus, Sandra M. Bachand, William R. Horwath, Philip A.M. BachandDirect and indirect effects of tides on ecosystem-scale CO2 exchange in a brackish tidal marsh in Northern California
We investigated the direct and indirect influence of tides on net ecosystem exchange (NEE) of carbon dioxide (CO2) in a temperate brackish tidal marsh. NEE displayed a tidally driven pattern with obvious characteristics at the multiday scale, with greater net CO2uptake during spring tides than neap tides. Based on the relative mutual information between NEE and biophysical variables, this was drivAuthorsSara Knox, Lisamarie Windham-Myers, Frank Anderson, Cove Sturtevant, Brian A. BergamaschiUse of flow cytometry and stable isotope analysis to determine phytoplankton uptake of wastewater derived ammonium in a nutrient-rich river
Anthropogenic alteration of the form and concentration of nitrogen (N) in aquatic ecosystems is widespread. Understanding availability and uptake of different N sources at the base of aquatic food webs is critical to establishment of effective nutrient management programs. Stable isotopes of N (14N, 15N) are often used to trace the sources of N fueling aquatic primary production, but effective useAuthorsCalla M. Schmidt, Tamara E. C. Kraus, Megan B. Young, Carol Kendall - Web Tools
Below are data or web applications associated with this project.
Bay-Delta Water Quality Survey, 2018 and 2020 Comparison
Delta Survey Data Visualization Contents for 2018 and 2020
Bay- Delta Water Quality, Nutrient and Phytoplankton Mapping | US Geological Survey
Data visualization tool created for California's Bay-Delta Regional Monitoring Program. This web applicaton visualizes nutrients and phytoplankton spatially and temporally.
Assessing Phytoplankton and Nutrient Abundance in the San Francisco Estuary and Delta
A data visualizatoin exploring the relationship between nutrient distribution and phytoplankton under different conditions across the San Francisco Delta and Estuary. Assessing distribution and abundance aids understanding of how managing nutrient supplies affects aquatic food webs, helping managers evaluate the potential environmental benefits of future nutrient reduction efforts agains
- News
Below are news stories associated with this project.
- Partners
Below are partners associated with this project.