Subsurface Science
PNNL is recognized internationally for providing scientific leadership to the Subsurface Biogechemical Research (SBR) for DOE's Office of Biological and Environmental Research (BER) in understanding energy and material transfer in the subsurface from molecular to field scales. We use cutting-edge laboratory and field research in a synergistic manner to help resolve critical subsurface science issues at DOE sites such as Hanford.
Current research is being performed within the Subsurface Science Scientific Focus Area and in DOE Integrated Field Research Challenge sites at Hanford and Rifle, Colorado sites.
Subsurface Science Focus Area (SFA)
A key goal of PNNL's research in subsurface science is to understand energy and material transfer in the subsurface from molecular to field scales. Much of our work is performed within the SESP's Subsurface Science Focus Area (SFA). The goals of the SFA are to develop
- An integrated conceptual model for microbial ecology in the Hanford subsurface and its influence on contaminant migration
- Fundamental understanding of chemical reaction, biotransformation, and physical transport processes in microenvironments and transition zones
- Quantitative biogeochemical reactive transport models for Tc, U, and Pu that integrate multi-process coupling at different spatial scales for field-scale application
We perform the following research for the SFA:
Biomolecular Studies of Microbiological Processes Controlling Contaminant Fate and Transport
Objectives
- Identify key microorganisms and/or consortia involved in the biogeochemical cycling of metals and site-relevant contaminants
- Elucidate biological mechanisms catalyzing the reductive valence transformations and pathways controlling the microscale distributions of metals (Fe) and contaminants (U, Tc) in Hanford subsurface sediments
We are performing genetic and physiological characterizations of DOE and Hanford Site-relevant subsurface microbial isolates and consortia. Our research focuses on single-organism investigations to understand the molecular mechanisms involved in metal and radionuclide biotransformation, particularly reduction reactions. We will identify genes, pathways, and subsystems involved in those key reactions, which will ultimately result in developing a comprehensive cross-species model of biological mechanisms.
Our integrative approach to studying the molecular mechanisms of metal and radionuclide biotransformation uses a combination of genetic, biochemical, and cultivation approaches with high-throughput proteomic and genomic technologies.
Saffarini and Löffler provide their expertise in molecular biology and ecology of metal-reducing organisms, respectively, to identify metal-reducing genes in Hanford-relevant organisms. Our research is closely coordinated with the molecular-scale projects that are isolating and characterizing redox active proteins, and pore-scale projects that are exploring biogeochemical processes controlling speciation of U and Tc in sediments and mineral separates from Hanford.
Research Team
Alex Beliaev, Daâd Saffarini (University of Wisconsin-Madison), and Frank Löffler (Georgia Tech).
Pore-Scale Biogeochemical Processes Controlling Contaminant Fate & Transport
Objective
- Characterize biogeochemical reaction mechanisms and rates controlling U and Tc speciation and distribution and Fe and Mn mineral reactivities at the pore-scale in Hanford subsurface sediments
Scope
- Experimental investigations of metal and radionuclide transformations with microorganisms and reactive minerals (initial focus on valence changes) emphasizing microscale gradients and analyses to define them.
Research Team
Jim Fredrickson (PNNL): geomicrobiology, contaminant biogeochemistry, Matt Marshall (PNNL): microbiology, molecular biology, Ji-Hoon Lee (PNNL): geomicrobiology, Alice Dohnalkova (EMSL): microscopy, Eric Roden (UW-Madison): microscale redox cycling, Ken Kemner/Steve Heald (ANL-APS): X-ray spectroscopy and microscopy
Microbial Ecology
This project has two primary components: a census of Hanford subsurface microbial communities, and experimental manipulations of microbial communities or relevant single organisms under simulated natural conditions or in situ. The census will use a suite of culture-independent methods (16S rRNA gene analyses, quantitative PCR of specific functional groups of microbes, and proteomic analyses) to assay the relative abundance of different microbes across natural gradients and transition zones and determine the functional proteins expressed by the organisms. Cultivation techniques that emphasize exposure to low nutrient fluxes typical of subsurface environments will be applied in parallel to obtain and characterize Hanford-relevant microbes.
Key outputs from this project will be relevant cultures and processes for detailed investigation and experiments in other SFA projects. Differences in community composition will be related to geological, geochemical and biogeochemical activity features via new data mining tools (Knight). These will form the basis for hypotheses that drive experimental manipulations in which natural communities or Hanford-relevant organisms are incubated in subsurface sediments either in laboratory columns or deployed in boreholes.
We anticipate that spatial and temporal heterogeneities in terminal electron acceptors (particularly O2 and Fe or Mn oxides) will affect the fate and transport of U or Tc. These experiments will interface with molecular-scale studies to determine the extent to which biogeochemically reactive cell components identified in the laboratory are expressed under natural conditions that can test their model predictions.
Research Team
Allan Konopka (PNNL), PI and R. Knight (U of Colorado), bioinformatics and data analysis
Functional Characterization of Microbial Macromolecules
Extracellular electron transfer pathways of Shewanella oneidensis MR-1 (Fredrickson et. al., 2008)
Microbial macromolecules with electron transfer capability affect the valence states of U and Tc contaminants as part of biogeochemical processes
Objective: To understand the molecular mechanisms by which microbial macromolecules (e.g. redox proteins) engage and react with U and Tc contaminants.
Scope: Molecular characterization of the redox-active biomolecule-facilitated electron transfer processes that are used for valence transformation of U and Tc in the cell envelope of Hanford-relevant microorganisms.
Research Team
Liang Shi (PNNL), gene cloning, protein purification and characterization, David Richardson (U of East Anglia), protein structure and function studies, Zheming Wang (PNNL), U and Fe reactions, and Dave Kennedy (PNNL), U and Fe reactions