Biogeochemistry Group Active
Hydrologic technicians deploying a flow sensor on a shoal in San Francisco Bay to investigate phytoplankton production and nutrient transformations.
A view from the office: USGS scientists heading out to deploy sensors for sediment nutrient storage and release in Rodeo Lagoon.
USGS laboratory technician filtering for chlorophyll-a.
Scientists aboard research vessel Aiken conduct water-quality mapping in support of wastewater-derived nutrients project.
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.
Nitrogen Dynamics Along the Sacramento River and Links to Phytoplankton Dynamics: Resolving Spatial and Temporal Variability Using In-Situ, High-Frequency Measurements and Other Tools
Interactions Between Physical Processes and Suspended Sediment Quality in Relation to Spawning Migrations of Delta Smelt
Causes and Relevance of Phytoplankton Blooms in the Northern Sacramento-San Joaquin Delta
Low Intensity Chemical Dosing (LICD)
Effects of Aquatic Vegetation on Water Quality and Residence Time in the Bay-Delta
Transport of dissolved organic matter by river networks from mountains to the sea: a re-examination of the role of flow across temporal and spatial scales
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Below are publications associated with this project.
Potential for negative emissions of greenhouse gases (CO2, CH4 and N2O) through coastal peatland re-establishment: Novel insights from high frequency flux data at meter and kilometer scales
Using paired in situ high frequency nitrate measurements to better understand controls on nitrate concentrations and estimate nitrification rates in a wastewater-impacted river
Irrigation as a fuel pump to freshwater ecosystems
An introduction to high-frequency nutrient and biogeochemical monitoring for the Sacramento–San Joaquin Delta, northern California
Synthesis of data from high-frequency nutrient and associated biogeochemical monitoring for the Sacramento–San Joaquin Delta, northern California
Clearing the waters: Evaluating the need for site-specific field fluorescence corrections based on turbidity measurements
A river-scale Lagrangian experiment examining controls on phytoplankton dynamics in the presence and absence of treated wastewater effluent high in ammonium
Effects of solid-liquid separation and storage on monensin attenuation in dairy waste management systems
Using continuous underway isotope measurements to map water residence time in hydrodynamically complex tidal environments
Forecasting tidal marsh elevation and habitat change through fusion of Earth observations and a process model
Assessing wildlife benefits and carbon storage from restored and natural coastal marshes in the Nisqually River Delta: Determining marsh net ecosystem carbon balance
Optical properties of dissolved organic matter (DOM): Effects of biological and photolytic degradation
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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
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: 18Nitrogen Dynamics Along the Sacramento River and Links to Phytoplankton Dynamics: Resolving Spatial and Temporal Variability Using In-Situ, High-Frequency Measurements and Other Tools
The overall project objective is to further our understanding of the link between nitrogen and phytoplankton dynamics in the Sacramento River and to elucidate effects of wastewater treatment plant effluent on food web dynamics.Interactions Between Physical Processes and Suspended Sediment Quality in Relation to Spawning Migrations of Delta Smelt
The proposed study is designed to better establish relationships between patterns of delta smelt abundance and properties of suspended particles as measured by optical and acoustical techniques.Causes and Relevance of Phytoplankton Blooms in the Northern Sacramento-San Joaquin Delta
Phytoplankton are an important part of aquatic food webs and ecosystems. These single-celled plants grow faster in the stronger light of spring or summer, resulting in population explosions called phytoplankton blooms. These blooms in turn feed zooplankton (free-floating aquatic microorganisms), providing food for many aquatic species, including fish, shrimp, crabs, and other invertebrates.Low Intensity Chemical Dosing (LICD)
Rivers, wetlands, and agricultural operations supply natural organic material to the Sacramento-San Joaquin Delta (Delta) and the San Francisco Estuary. This natural organic matter provides many ecosystem benefits, but it also adversely affects drinking water. During drinking water treatment, chlorine added for purposes of pathogen control reacts with dissolved organic carbon (DOC) in the water to...Effects of Aquatic Vegetation on Water Quality and Residence Time in the Bay-Delta
The spread of invasive aquatic vegetation in the Sacramento-San Joaquin Delta is having a profound impact on the Delta’s natural habitat. The presence of these “aquatic weeds” has been shown to alter water velocity and increase water clarity, posing threats to native fish species, specifically the threatened Delta Smelt. These aquatic plants can also affect the foodweb by altering nutrient...Transport of dissolved organic matter by river networks from mountains to the sea: a re-examination of the role of flow across temporal and spatial scales
The transport of dissolved organic matter (DOM) by rivers is an important component of the global carbon cycle, affects ecosystems and water quality, and reflects biogeochemical and hydrological processes in watersheds. Understanding the fundamental relationships between discharge and DOM concentration and composition reveals important information about watershed flow paths, soil flushing, connect - Multimedia
Below are multimedia items associated with this project.
- Publications
Below are publications associated with this project.
Filter Total Items: 69Potential for negative emissions of greenhouse gases (CO2, CH4 and N2O) through coastal peatland re-establishment: Novel insights from high frequency flux data at meter and kilometer scales
High productivity temperate wetlands that accrete peat via belowground biomass (peatlands) may be managed for climate mitigation benefits due to their global distribution and notably negative emissions of atmospheric carbon dioxide (CO2) through rapid storage of carbon (C) in anoxic soils. Net emissions of additional greenhouse gases (GHG)—methane (CH4) and nitrous oxide (N2O)—are more difficult tAuthorsLisamarie Windham-Myers, Brian A. Bergamaschi, Frank A. Anderson, Sarah Knox, Robin Miller, Roger FujiiUsing paired in situ high frequency nitrate measurements to better understand controls on nitrate concentrations and estimate nitrification rates in a wastewater-impacted river
We used paired continuous nitrate ( ) measurements along a tidally affected river receiving wastewater discharge rich in ammonium ( ) to quantify rates of change in  concentration ( ) and estimate nitrification rates.  sensors were deployed 30 km apart in the Sacramento River, California (USA), with the upstream station located immediately above the regional wastewater treatment plant (WWTP). We uAuthorsTamara E. C. Kraus, Katy O'Donnell, Bryan D. Downing, Jon R. Burau, Brian A. BergamaschiIrrigation as a fuel pump to freshwater ecosystems
We generated a detailed time series of total dissolved hydrolyzable amino acids (DHAA) in a watershed dominated by irrigated agriculture in northern California, USA to investigate the roles of hydrologic and seasonal changes on the composition of dissolved organic matter (DOM). DHAA are sensitive indicators of the degradation state and reactivity of DOM. DHAA concentrations ranged from 0.55 to 9.9AuthorsSandrine Matiasek, Brian A. Pellerin, Robert G.M. Spencer, Brian A. Bergamaschi, Peter J. HernesAn introduction to high-frequency nutrient and biogeochemical monitoring for the Sacramento–San Joaquin Delta, northern California
Executive SummaryThis report is the first in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Joaquin Delta of northern California (Delta). This first report provides an introduction to the reasons for and fundamental concepts behind collecting HF measurements, and describes the benefits associated with a realAuthorsTamara E.C. Kraus, Brian A. Bergamaschi, Bryan D. DowningSynthesis of data from high-frequency nutrient and associated biogeochemical monitoring for the Sacramento–San Joaquin Delta, northern California
Executive SummaryThis report is the second in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Joaquin Delta of northern California (Delta). The purpose of this report is to synthesize the data available from a nutrient and water-quality HF (about every 15 minutes) monitoring network operated by the U.S. GeoloAuthorsBryan D. Downing, Brian A. Bergamaschi, Tamara E.C. KrausClearing the waters: Evaluating the need for site-specific field fluorescence corrections based on turbidity measurements
In situ fluorescent dissolved organic matter (fDOM) measurements have gained increasing popularity as a proxy for dissolved organic carbon (DOC) concentrations in streams. One challenge to accurate fDOM measurements in many streams is light attenuation due to suspended particles. Downing et al. (2012) evaluated the need for corrections to compensate for particle interference on fDOM measurements uAuthorsJohn Franco Saraceno, James B. Shanley, Bryan D. Downing, Brian A. PellerinA river-scale Lagrangian experiment examining controls on phytoplankton dynamics in the presence and absence of treated wastewater effluent high in ammonium
Phytoplankton are critical component of the food web in most large rivers and estuaries, and thus identifying dominant controls on phytoplankton abundance and species composition is important to scientists, managers, and policymakers. Recent studies from a variety of systems indicate that ammonium ( NH+4) in treated wastewater effluent decreases primary production and alters phytoplankton speciesAuthorsTamara E. C. Kraus, Kurt D. Carpenter, Brian A. Bergamaschi, Alexander Parker, Elizabeth B. Stumpner, Bryan D. Downing, Nicole Travis, Frances Wilkerson, Carol Kendall, Timothy MussenEffects of solid-liquid separation and storage on monensin attenuation in dairy waste management systems
Environmental release of veterinary pharmaceuticals has been of regulatory concern for more than a decade. Monensin is a feed additive antibiotic that is prevalent throughout the dairy industry and is excreted in dairy waste. This study investigates the potential of dairy waste management practices to alter the amount of monensin available for release into the environment. Analysis of wastewater aAuthorsSarah C. Hafner, Naoko Watanabe, Thomas Harter, Brian A. Bergamaschi, Sanjai J. ParikhUsing continuous underway isotope measurements to map water residence time in hydrodynamically complex tidal environments
Stable isotopes present in water (δ2H, δ18O) have been used extensively to evaluate hydrological processes on the basis of parameters such as evaporation, precipitation, mixing, and residence time. In estuarine aquatic habitats, residence time (τ) is a major driver of biogeochemical processes, affecting trophic subsidies and conditions in fish-spawning habitats. But τ is highly variable in estuariAuthorsBryan D. Downing, Brian A. Bergamaschi, Carol Kendall, Tamara E. C. Kraus, Kate J. Dennis, Jeffery A. Carter, Travis von DessonneckForecasting tidal marsh elevation and habitat change through fusion of Earth observations and a process model
Reducing uncertainty in data inputs at relevant spatial scales can improve tidal marsh forecasting models, and their usefulness in coastal climate change adaptation decisions. The Marsh Equilibrium Model (MEM), a one-dimensional mechanistic elevation model, incorporates feedbacks of organic and inorganic inputs to project elevations under sea-level rise scenarios. We tested the feasibility of deriAuthorsKristin B. Byrd, Lisamarie Windham-Myers, Thomas Leeuw, Bryan D. Downing, James T. Morris, Matthew C. FernerAssessing wildlife benefits and carbon storage from restored and natural coastal marshes in the Nisqually River Delta: Determining marsh net ecosystem carbon balance
Working in partnership since 1996, the U.S. Fish and Wildlife Service and the Nisqually Indian Tribe have restored 902 acres of tidally influenced coastal marsh in the Nisqually River Delta (NRD), making it the largest estuary-restoration project in the Pacific Northwest to date. Marsh restoration increases the capacity of the estuary to support a diversity of wildlife species. Restoration also inAuthorsFrank Anderson, Brian A. Bergamaschi, Lisamarie Windham-Myers, Isa Woo, Susan De La Cruz, Judith Z. Drexler, Kristin Byrd, Karen M. ThorneOptical properties of dissolved organic matter (DOM): Effects of biological and photolytic degradation
Advances in spectroscopic techniques have led to an increase in the use of optical properties (absorbance and fluorescence) to assess dissolved organic matter (DOM) composition and infer sources and processing. However, little information is available to assess the impact of biological and photolytic processing on the optical properties of original DOM source materials. We measured changes in commAuthorsAngela Hansen, Tamara E. C. Kraus, Brian Pellerin, Jacob Fleck, Bryan D. Downing, Brian A. Bergamaschi - Web Tools
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- News
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- Partners
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