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Subsurface Biogeochemical Research Program

Performance Measures and Milestones FY 2006

(SC GG 5.21.1)

Develop predictive model for contaminant transport that incorporates complex biology, hydrology, and chemistry of the subsurface. Validate model through field

First Quarter Results

This report summarizes the most recent results of the research project “Stability of U(VI) and Tc(VII) Reducing Microbial Communities to Environmental Perturbation: Development and Testing of a Thermodynamic Network Model” that is attempting to model (predict) the effect of exogenous chemical amendments on the subsurface microbial community at the Oak Ridge Field Research Center (FRC). The model explicitly couples the thermodynamics of microbial growth and geochemical reactions to make quantitative system-specific predictions of microbial community dynamics. Model predictions are being tested with the results of small- to intermediate-scale field experiments.

1. Overall Objective and Hypothesis

The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on the composition and functional stability of subsurface microbial communities. The overall scientific hypothesis is that a thermodynamic analysis of the energy-yielding reactions performed by broadly defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition and system geochemistry (including contaminant chemistry) that occur when a substrate is added to the subsurface or when environmental conditions change.

2. Types of Investigations Performed

Our research consists of three main activities:

  • Model Development: A list of the major microbial groups present in samples of groundwater and sediment from the FRC has been compiled. Computer programs have been developed to compute the overall growth reaction and governing thermodynamic quantities for each group. Necessary model input parameters (electron transfer efficiencies) are being estimated from large numbers of published laboratory experiments. The output from this activity is a thermodynamic data base containing the chemical stoichiometry and standard state free energy change that defines the growth of each group (e.g. denitrifiers, iron reducers, etc.). Collectively these calculations define the growth reactions and energy flows in an intact microbial community.
  • Numerical Simulations: The thermodynamic data base is combined with existing geochemical data and used to predict equilibrium reaction paths that show the coupled changes in microbial community composition and system geochemistry that occur when amendments are added to the subsurface. Simulations are being performed to investigate the effect of ethanol additions on uranium and technetium bioimmobilization for the major subsurface environments at the FRC (Areas 1 and 3 with neutral pH and low nitrate groundwater; and Area 2 with low pH and high nitrate groundwater). Inputs include measured chemical quantities on sediment and groundwater; outputs include predicted changes in groundwater and sediment chemistry and microbial community composition. Model predictions have been consistent with field observations and provide important insights into the role of specific microbial groups (esp. denitrifiers) on overall system response. Model predictions are being used to investigate alternate bioimmobilization strategies (choice of substrate, sulfate additions, etc.) and to predict the long-term stability of bioreduced uranium and technetium to changing environmental conditions.
  • Experimental Verification: Ultimately model predictions must be verified by direct measurement and we have assembled a suite of lipid and nucleic acid-based biomarkers for this purpose. We are developing a “dictionary” that will allow predicted growth of defined microbial groups to be detected and quantified by one or more distinct biomarkers. Model predictions for long-term experiments in small-scale microcosms and intermediate-scale physical models and for short-term small-scale field experiments are being compared with biomarker data collected on groundwater and sediment samples. Initial comparisons are made on total biomass and groups with known functional genes. Particular emphasis is placed on denitrifiers, sulfate reducers, and iron reducers as these make up the largest portion (> 90 % in some cases) of the entire community following substrate addition. We are actively collaborating with several NABIR investigators to apply model simulations to other experimental systems.

3. Main Results

The most recent results of our project are summarized here:

  • The predicted microbial community composition varies greatly from one site to the next in response to electron donor additions. Principal factors are the concentrations of available electron acceptors, primarily oxygen, nitrate, sulfate, iron, and manganese.
  • Denitrification, fermentation, and sulfate-, iron-, and manganese-reduction are the major microbial processes in all environments tested.
  • pH has a relatively small effect on microbial community response to donor addition. Microbial bicarbonate production rapidly increases the pH in initially low pH environments.
  • Low concentrations of uranium and technetium provide very little energy to microorganisms and microbial uranium and technetium reduction consume only trivial amounts of added electron donor.
  • Bioreduced uranium can be readily reoxidized by oxidized groundwater once electron donor additions ceases; bioreduced technetium is more resistant to reoxidation

4. Planned Activities:

The activities planned for the coming year include:

  • We are continuing to refine the numerical model to include additional groups of microorganisms and additional microbial processes to better align the model with observations from laboratory and field experiments. In particular we wish to include groups that are involved in the oxidation of sulfide, ferrous iron, and bioreduced uranium.
  • We will design a series of laboratory microcosm experiments to explicitly test model predictions for a range of defined conditions. In these experiments, sufficient data will be collected to monitor changes in geochemistry and microbial community composition during both bioreduction and reoxidation.
  • We will collaborate with other NABIR investigators to test the model’s utility for interpreting laboratory and field data and for transferring results from one system to another.
  • A series of numerical simulations will be conducted to quantify the stability of an intact microbial community to various environmental perturbations including changing pH, nitrate concentration, and donor availability.

5. Project Significance:

This project is clearly showing that the ability to predict the effects of donor addition on change in microbial community composition is essential for creating conditions that favor the long-term stability of bioreduced uranium and technetium. Moreover, the ability of a microbial community to maintain functional stability (i.e. maintain high rates of uranium and technetium reduction) when subjected to various environmental perturbations is of critical importance for the ultimate use of bioimmobilization at DOE legacy waste sites. The longer-term significance of this project will be to provide a comprehensive theoretical framework for designing and interpreting complex field experiments and to aid in “bridging-the-gap” between basic research and field applications.

  • DE-FOA-0002482 - Integrated Computational and Data Infrastructure for Scientific Discovery
    Now accepting applications. Letters of Intent Due: April 2, 2021, 5:00 p.m. Eastern Time
  • Office of Science Graduate Student Research (SCGSR) Program 2021 Solicitation 1
    Now accepting applications. Pre-Application Due: May 5, 2021, 5:00 p.m. Eastern Time
  • DE-FOA-0002431 – DOE EPSCoR (Experimental Program to Stimulate Competitive Research) Implementation Grants
    Now accepting applications. Pre-Application Due: December 15, 2020, 5:00 p.m. Eastern Time
  • DE-FOA-0002392-Environmental System Science
    Now accepting applications. Pre-Application Due: Dec. 17, 2020, 5:00 p.m. Eastern Time
  • ASCR Leadership Computing Challenge
    Call for Proposals Open. Pre-Proposals Due: January 4, 2021, 5:00 pm Eastern Time
  • Environmental Research Funding: DoD SERDP
    Now accepting applications.
    • Core Solicitation for Environmental Research and Development Proposals. Pre-Proposals Due: Jan. 7, 2021, 2:00 p.m. Eastern Time.
    • SEED Solicitation. Proposals Due: March 4, 2021, 2:00 p.m. Eastern Time. [11/9]
  • DE-FOA-0002431-Established Program To Stimulate Competitive Research (DOE EPSCoR) Implementation Grants
    Now accepting applications. Pre-Application Due: Dec. 15, 2020, 5:00 p.m. Eastern Time
  • Office of Science Graduate Student Research (SCGSR) Program 2020 Solicitation 2
    Now accepting applications. Pre-Application Due: Nov. 12, 2020, 5:00 p.m. Eastern Time
  • See Also:

PI-Submitted Research Highlights for Subsurface Biogeochemical Research Program

Now Featuring

Open Watershed Science by Design Workshop Report

October 2019

EESSD Strategic Plan 2018

Download PDF

Subsurface Biogeochemical Research Overview

November 2019 [PDF]