James Fredrickson | Environmental Molecular Sciences Laboratory

Role of Microenvironments and Transition Zones in Field Scale Microbial Ecology and Biogeochemistry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

Project type

Limited Scope

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science…

Influences of Hydrologic Exchange Flows on River Corridor and Watershed Biogeochemical Function

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Stegen

We are developing predictive understanding of the processes that govern influences of hydrologic exchange flows on water quality, nutrient dynamics, and ecosystem health in dynamic river corridor…

The Role of Microenvironments and Physicochemical Subsurface Components on Field Scale Biogeochemistry and Contaminant Mobility

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

Project type

Exploratory Research

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science…

Deinococcus Radiodurans for Bioremediation - Non-nuclear (PNNL #27197)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Fredrickson

Project type

Exploratory Research

Need ICP-MS analysis of cell extracts to quantify microbial uptake of various metals including Fe, Mn, and Cd.

Linking Microbial Communities to Subsurface Geochemistry and Hydrology at the Field-Scale

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Stegen

Project type

Large-Scale EMSL Research

Background and Key Challenges: A major challenge in subsurface science is understanding how microbial communities, geochemistry, and hydrology interactively govern the fate and transport of…

Environmental Sensing, Metabolic Response,Regulatory Network (PNNL 42654, BES)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Fredrickson

Project type

Exploratory Research

HPLC analysis and quanitation of organic acids is a critical tool to track metabolic changes during growth in microbial cultures. Because are own HPLC system has ended it's useful life, Tom…

Untangling the Complexity of Microbial Networks by Using Simplified Natural Communities

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

H Wiley

The overall goal of this proposal is to understand the dynamics of both microbial populations and their gene regulatory networks in response to environmental perturbations and to elucidate mechanisms…

Grand Challenge in Biogeochemistry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Fredrickson

Project type

Grand Challenge

Do multiheme cytochromes associated with the outer membrane of metal reducing bacteria (mtrC in Shewanella oneidensis and omcB in Geobacter sulfurreducens, for example) transfer electrons to Fe(III)…

Role of Microenvironments and Transition Zones in Subsurface Reactive Contaminant Transport

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science…

Thrust Area 3:Mutagenesis and Functional Characterization of Shewanella oneidensis Genes Involved in Fe(III) and Mn(IV) Oxide Reduction (LDRD #3)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alex Beliaev

Project type

Grand Challenge

Although microbial metal reduction has been extensively studied from standpoints of ecology, physiology, genetics and biochemistry, little is known about the molecular mechanisms and pathways of…

Biological Systems Interactions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Fredrickson

SPECIFIC AIMS: The overall objective of the proposed research is to acquire a predictive understanding of how microbial interactions impart stability, fitness, and functional efficiency to microbial…

Microbial Reduction of Illite and Glauconite

Lead Institution

Miami University

Principal Investigator

Hailiang Dong

Project type

Exploratory Research

This project investigates reduction of Fe(III) in structure of sedimentary illite and glauconite by Shewanella oneidensis CN32, and possible implications for bioremediation and subsurface microbial…

Untangling the complexity of phototroph-heterotroph interactions in the lab and in the field

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

H Wiley

Project type

Large-Scale EMSL Research

Despite the fact that ubiquitous microbial interspecies interactions form the foundation of energy flow as well as the biogeochemical cycling of carbon and other elements within natural environments,…

Observation of Biogenic Nano-scaled Wire-like Arsenic Sulfide Mineral

Lead Institution

Gwangju Institute of Science and Technology (GIST)

Principal Investigator

Ji-hoon Lee

Project type

Capability Research

A facultative anaerobic rod, dissimilatory iron-reducing bacterium, Shewanella sp. strain HN-41, which was isolated from a oil shale rock fragment collected at a tidal in Haenam, South Korea, was…

Role of Microenvironments and Transition Zones in Subsurface Reactive Contaminant Transport

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science…

Shewanella oneidensis

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Project type

Exploratory Research

Bacterial strains such as Shewanella oneidensis strain MR-1 are key organisms in the bioremediation of metals due to their ability to enzymatically reduce and precipitate a diverse range of heavy…

Quantifying the functional and structural states of dynamic microbial communities

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Fredrickson

Project type

Large-Scale EMSL Research

The overall goal of this proposal is to provide a quantitative framework in which to compare species-resolved patterns of gene expression, allowing comparison of the effects of perturbations of…

MICROSCALE METABOLIC, REDOX AND ABIOTIC REACTIONS IN HANFORD 300 AREA SUBSURFACE SEDIMENTS

Lead Institution

Washington State University

Principal Investigator

Haluk Beyenal

Project type

Exploratory Research

This proposal is the NMR component of a funded DOE/ERSP program project in which we proposed to use the Hanford 300 Area as a site for identifying microscale metabolic, abiotic and redox reactions in…

Coupling Microbial Communities to Carbon and Contaminant Biogeochemistry in the Groundwater-Surface Water Interaction Zone

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Stegen

Project type

FICUS Research

The proposed study will integrate molecular data generated through a combination of JGI and EMSL capabilities to support research activities under the Subsurface Biogeochemical Research-Science Focus…

Role of Microenvironments and Transition Zones in Subsurface Reactive Contaminant Transport

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

Project type

Exploratory Research

The PNNL Scientific Focus Area (SFA) will resolve critical Hanford and basic subsurface science issues through integrated, multi-disciplinary, science-theme focused research on the role of…

Hydro-Biogeochemical Process Dynamics in the Groundwater-Surface Water Interaction Zone

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Zachara

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL.PNNL Scientific Focus Area. The PNNL SFA will develop a predictive understanding…

Microscale Metabolic, Redox and Abiotic Reactions in Hanford 300 Area Subsurface Sediments

Lead Institution

Washington State University

Principal Investigator

Haluk Beyenal

Project type

Large-Scale EMSL Research

This proposal is the NMR component of a funded DOE/ERSP program project in which we proposed to use the Hanford 300 Area as a site for identifying microscale metabolic, abiotic and redox reactions in…

Biosystems Analysis for Determining the Impact of Nutrient Uptake on Autotroph-Heterotroph Interactions within Cyanobacterial Consortia

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

Project type

Large-Scale EMSL Research

The exchange of carbon and other nutrients between microorganisms is a key factor in the establishment of microbial interactions and trophic levels. Depending upon the nutrient, the establishment of…

Regulatory dynamics of microbial communities

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

H Wiley

Project type

Large-Scale EMSL Research

This is a proposal to conduct work in EMSL in support of the Foundational Scientific Focus Area (FSFA) research program at Pacific Northwest National Laboratory. This large-scale research program…

Hydro-Biogeochemical Process Dynamics in the Groundwater-Surface Water Interaction Zone

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Zachara

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL.PNNL Scientific Focus Area. The PNNL SFA will develop a predictive understanding…

Modeling complex bacterial cell systems through development of segregated models with spatial localization

Lead Institution

Oregon State University

Principal Investigator

Brian Wood

Project type

Exploratory Research

Systems of cells can exhibit behavior that is more complex than is expressed by individuals within the population. An example here might the be the formation of biofilms on surfaces. Because of the…

Deciphering electron transfer in biofilm communications by in situ chemical imaging

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

Xiao-Ying Yu

We seek to understand how the dynamics of nutrients, metabolites, and solid surface influence microbial processes in biofilm systems. Our overarching hypothesis is that biophysical and biochemical…

(gc3603)Image Processing, Modeling and Simulation of Complex Biological Systems Using Volume Filling and Boundary Fitted Mesh Based Methods

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Harold Trease

Project type

Capability Research

Terascale hardware and software capabilities represent a large increment in our ability to apply modeling and simulation to solving biology problems that include both spatially and temporally…

Influences of Hydrologic Exchange Flows on River Corridor and Watershed Biogeochemical Function

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Stegen

We are developing predictive understanding of the processes that govern influences of hydrologic exchange flows on water quality, nutrient dynamics, and ecosystem health in dynamic river corridor…

Role of Microenvironments and Transition Zones in Field scale microbial ecology and biogeochemistry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

Project type

Exploratory Research

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science…

Influences of Hydrologic Exchange Flows on River Corridor and Watershed Biogeochemical Function

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Stegen

We are developing predictive understanding of the processes that govern influences of hydrologic exchange flows on water quality, nutrient dynamics, and ecosystem health in dynamic river corridor…

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