Microbial Community Structure and Function in Response to Accelerated Bioremediation of Subsurface Uranium

EPA Grant Number: FP916933
Title: Microbial Community Structure and Function in Response to Accelerated Bioremediation of Subsurface Uranium
Investigators: Daly, Rebecca Anne
Institution: University of California - Berkeley
EPA Project Officer: Michaud, Jayne
Project Period: August 1, 2008 through August 1, 2011
RFA: STAR Graduate Fellowships (2008) RFA Text |  Recipients Lists
Research Category: Academic Fellowships


Oxidized uranium, U(VI) is highly soluble and toxic. Current remediation strategies of toxic metals and radionuclides utilize microbially-mediated reductive precipitation and complexation to immobilize metals. A promising, low-cost strategy for U remediation is through microbially mediated reduction of U(VI) to insoluble U(IV) by indigenous microbial communities. This natural process is accelerated by delivery of organic carbon into the subsurface sediment and groundwater. Carbon amendment lowers the local redox potential, stimulates microbial growth and acts as both electron donor and carbon source for microorganisms. The bioremediation process is dependent on three measurable factors: the geochemical environment, microbial community structure and microbial community function. Delineating the relationships and interactions among these factors is recognized to be crucial for the application of successful accelerated bioremediation. The objectives of my research are to:

  • Determine if the trajectories of microbial community structure and function following carbon amendment can be related to, and predicted by, key environmental parameters.
  • Assess the relative importance of the characteristics of the indigenous microbial community, sediment, groundwater, and concentration of carbon amendment as the major determinants of microbial community functional response and bioremediation capacity.


The basic framework of my research is to follow microbial community functional and phylogenetic trajectories:

  • Starting with identical physical/chemical conditions – but different initial microbial communities.
  • Starting with the same initial microbial community but different rates of carbon amendment and physical/chemical conditions.
A full factorial design of 18 combinations of starting microbial communities, sediment matrix/water geochemistry and carbon supply will be tested as well as sterile controls. Sediments from three different U-contaminated sites will be used in small, easily replicated and manipulated flow-through cells. Microbial community trajectories will be followed using community DNA and RNA applied to a high-density phylogenetic microarrays (PhyloChip) and functional microarrays (GeoChip). Chemical analyses will be performed on effluent solutions and sediment subsamples, and redox status will be monitored. These results will be used for multivariate statistical analyses, in order to link community structure and function to environmental variables.

Expected Results:

Despite a large number of field- and laboratory-scale microbial analyses associated with U bioremediation, relatively little is known about how complex microbial communities change and interact with their environment during the process of bioremediation. The critical first step towards determining the level and type of microbial community information that represents a suitable parameter for input into models is identifying predictable responses in microbial systems. Such responses must be generalizable and predictable across a range of relevant conditions. The results from this study may provide the understanding and data required for successful modeling of subsurface remediation. By using U-contaminated sediments from three environmentally relevant sites, I will take the first steps to determine broadly significant, conserved microbial functions related to successful toxic metal and radionuclide bioremediation.

Supplemental Keywords:

uranium, bioremediation, microbial ecology, microbial community structure, microbial community function, biogeochemical modeling, environmental microbiology, DNA, RNA, microarrays,

Progress and Final Reports:

  • 2009
  • 2010
  • Final