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Understanding microbial dynamics in a biostimulated aquifer using combined Omics approaches

EMSL Project ID


At the Rifle Integrated Field Research Challenge (IFRC) site in Colorado, carbon amendments to the subsurface are used to stimulate growth of the indigenous microbial community. The microbial populations reduce groundwater U(VI) to sparingly soluble U(IV), decreasing its mobility. The dynamics between the biogeochemistry of the system and microbial community composition is complex. The activity of Fe(III)-reducing bacteria is typically stimulated within a day of acetate reaching a particular region of the aquifer, and persists as the dominant geochemical process for approximately 30 days. During this time however, a range of molecular and "omics"-based techniques have suggested that (1) the microbial community is more diverse than previously thought, and (2) a range of shifts occur within the microbial community, at both the family/genus and strain levels. The processes driving these biological shifts are poorly understood at present, but play a key role in determining the efficiency of stimulated processes, such as microbial U(VI) reduction. To date, proteomic techniques have been applied to planktonic biomass recovered from the aquifer at Rifle during biostimulation. We propose coupling this data to metatranscriptomic analysis, to elucidate the relationship between transcription and translation during carbon amendment, and to potentially reveal regulatory mechanisms that operate at the RNA level. These data will contribute towards a greater understanding of the community function and evolution as biostimulation progresses. Temporally resolved samples will be recovered from the aquifer at Rifle during field experiments where different electron donors are injected into the subsurface. This information will aid the eventual aim of having a level of control over microbial communities, such that they can be stimulated to perform specific processes that are desired in the environment.

Project Details

Project type
Large-Scale EMSL Research
Start Date
End Date


Principal Investigator

Jillian Banfield
University of California, Berkeley

Team Members

Kelly Wrighton
Colorado State University

Michael Wilkins
Colorado State University

Kenneth Williams
Lawrence Berkeley National Laboratory

Philip Long
Lawrence Berkeley National Laboratory

Mary Lipton
Environmental Molecular Sciences Laboratory

Related Publications

Castelle C, KC Wrighton, BC Thomas, LA Hug, CT Brown, MJ Wilkins, KR Frischkorn, SG Tringe, A Singh, LM Markillie, RC Taylor, KH Williams, and JF Banfield. 2015. "Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling." Current Biology. doi:10.1016/j.cub.2015.01.014
Long P E,Williams K H,Hubbard S S,Banfield J F 2016. "Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes" Trends in Microbiology
Nicora CD, BJ Anderson, SJ Callister, AD Norbeck, SO Purvine, JK Jansson, OU Mason, M David, DD Jurelevicius, RD Smith, and MS Lipton. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies ." Proteomics 13(18-19):2776-2785. doi:10.1002/pmic.201300003
Wrighton KC, BC Thomas, I Sharon, CS Miller, C Castelle, NC VerBerkmoes, MJ Wilkins, RL Hettich, MS Lipton, KH Williams, PE Long, and JF Banfield. 2012. "Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla." Science 337(6102):1661-1665. doi:10.1126/science.1224041