Research in the Wilkins lab focuses on interactions between microorganisms and their local environment. Microorganisms can catalyze a huge range of reactions, many of which directly or indirectly affect the chemistry and physical structure of the region they inhabit. We currently study some of these processes in a variety of different environments, with links to contaminant remediation (e.g. uranium), elemental cycling (carbon, sulfur), and hydrocarbon degradation (e.g. deep shale formations).
Microbial drivers of unique biogeochemistry in prairie pothole lakes
The Prairie Pothole area of the US and Canada spans a large portion of the Midwest/Great Northern Plains, and consists of many small wetlands that were formed during the retreat of glaciers over this region. Due to combined hydrologic and weathering processes, some of these lake sediments and pore waters contain some of the highest concentrations of dissolved organic carbon and sulfur species ever measured in fresh water systems. These geochemical conditions can potentially sustain a range of microbial processes, including sulfate-reduction, methanogenesis, and methane oxidation. In collaboration with Professor Yo Chin (OSU-EarthSciences) we are using a metagenomic framework to re-construct the microbial community functional network within prairie pothole sediments and pore waters. These data will subsequently be used to identify key biogeochemical processes in these systems that have implications for carbon degradation, pesticide breakdown, and methane production.
Microbial community dynamics and function in shallow subsurface aquifers
We are currently working in two shallow aquifers in the Western US, at Hanford, WA, and Rifle, CO. The Hanford 300 Area aquifer is located at the site of a former uranium processing facility in Eastern Washington State. Here, groundwater flowing through highly-transmissive sediments interacts with intruding river water from the nearby Columbia River. The nature of these interactions are currently under investigation, but are thought to impact groundwater geochemistry, with changes in dissolved organic carbon and conductivity reported. We are currently investigating the effects of these processes on indigenous microbial community structure and function, across both space and time scales using a range of techniques including 16S rRNA analyses, metagenomics, and proteomics.
The Rifle aquifer is located at the site of a former uranium milling plant in Western Colorado, and serves as a test-site for the application of multiple cutting-edge techniques for investigating subsurface biogeochemistry. Previous work at the site has used metagenomic techniques for identifying a fermentative role for novel bacterial phyla, and shotgun proteomic methods for determining the physiology and metabolism of dominant Geobacter species in the subsurface. We are currently involved in a collaborative effort with Lawrence Berkeley National Laboratory to understand the microbial function in natural ‘background’ sediments at the site. These materials contain a huge diversity of microbial species carrying out a large suite of reactions in the aquifer. Our current research is mainly focused on using proteomics to identify active metabolic pathways in native materials, and incorporate these results into biogeochemical reactive transport models that are being developed for the Rifle site.
Microbiology of deep shale formations
In collaboration with Dr. Paula Mouser (OSU-Civil, Environmental and Geodetic Engineering), Dr. David Cole (OSU-Earth Sciences), and Dr. Kelly Wrighton (OSU-Microbiology), we are investigating microbial diversity and function in deep shale formations in southeastern Ohio. These regions are currently the focus of great interest with regards to the extraction of natural gas via ‘fracking’. Using a suite of metagenomic, culturing, and stable isotope approaches, our aim is to determine indigenous microbial community structures in these extreme environments (high pressure, small pore size), and infer microbial function that allows for growth and survival in such systems.
- Wilkins MJ, Wrighton KC, Nicora, CD, Williams KH, McCue LA, Handley KM, Miller CS, Giloteaux L, Montgomery AP, Lovley DR, Banfield JF, Long PE & Lipton MS. (2013). Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface. PLoS One, 8(3): e57819. doi:10.1371/journal.pone.0057819
- Mouser PJ, Wilkins MJ, Smith D, Williams KH, Pasa-Tolic LJ & Long PE. (2013). Molecular characterization and utilization of dissolved organic matter by microbial communities indigenous to a uranium-contaminated aquifer. Biogeochemistry, Submitted.
- Fang Y, Wilkins MJ, Yabusaki SB, Lipton MS & Long PE. (2012). Evaluation of a genome-scale in silico metabolic model of Geobacter metallireducens using proteomic data from a field biostimulation experiment. Applied and Environmental Microbiology, 78:8735-8742
- Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE & Banfield JF. (2012). Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science, 337 1661
- Wilkins MJ, Callister SJ, Miletto M, Williams KH, Nicora CD, Lovley DR, Long PE & Lipton MS. (2011). Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI). Microbial Biotechnology, 4 55-63
- Callister SJ, Wilkins MJ, Lipton MS, Nicora CD, Williams KH, Banfield JF, VerBerkmoes NC, Hettich RL, N’Guessan AL, Mouser PJ, Elifantz H, Lovley DR & Long PE. (2010). Proteomics inferred legacy effects in the function and structure of biostimulated microbial communities. Environmental Science & Technology, 44 8897-8903.
- Wilkins MJ, VerBerkmoes NC, Williams KH, Callister SJ, Hettich RL, Lipton MS, Mouser PJ, Elifantz H, N’Guessan AL, Lovley DR, Long PE & Banfield JF. (2009). Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Applied and Environmental Microbiology, 75 6591-6599