The ENIGMA project seeks to discover, characterize the reciprocal interactions between the microbial communities and the geochemical and geophysical parameters of the shallow subsurface within the contamination plume of groundwater and sediment microbiomes in the shallow subsurface at the contaminated Oak Ridge Field Research Site (FRC). Our ambition is to do so at sufficient resolution to causally predict the active biotic and abiotic mechanisms mediating key processes such as denitrification; dissect the dispersing and persistent microbial community components critical in space and time during these processes, and ultimately predict the future changes in contaminant fate from current observations and possibly arising from natural and anthropogenic perturbations. Outcomes are significant both in the basic science of community ecology and in gaining an applied understanding of biologically-mediated subsurface processes in contaminated sediments. The FRC contains highly contaminated DOE legacy regions and excellent field infrastructure available for research instrumentation and 30+ years of biogeochemical data collected by other scientists. It has well-mapped hydrology and geology and complex gradients of nutrients, stressors, and contaminants, making the FRC an excellent site to study the reciprocal interactions of environmental factors on microbial ecology and activity. Across the site, a large number of active wells permit efficient groundwater sampling, and it is relatively cost-effective to drill new wells or retrieve depth-indexed sediment cores when the project requires it.
Relevant Publications
Mixed Nitrate and Metal Contamination Influences Operational Speciation of Toxic and Essential Elements - ENIGMA researchers compared the availability of elements in non-contaminated and acidic nitrate contaminated sediment and found that contamination impacted the bioavailability of essential elements. Relevant Publication →
Examining adaptations of a dominant bacterial species at a contaminated subsurface site - Leveraging comparative genomics, community analysis, and geochemical data to understand adaptations that facilitate survival of a dominant community member in the contaminated Oak Ridge Reservation subsurface. Relevant Publication →
Discovering microbial adaptations to subsurface niches - Gushgari-Doyle, S; L.M. Lui, T.N. Nielsen, X. Wu, R.G. Malana, F.L. Poole II, M.W.W. Adams, A.P. Arkin, R. Chakraborty (2022) Genotype to ecotype in niche environments: Adaptation of Arthrobacter to carbon availability and environmental conditions. ISME Comm. [DOI]:10.1038/s43705-022-00113-8 OSTI:1860268 Different niche micro-environments can affect the structure and function of microbial communities. Terrestrial subsurface environments exhibit specific biogeochemical conditions associated with… Relevant Publication →
Uncovering metal tolerance mechanisms using ENIGMA tools and Analysis - Thorgersen, M.P., .; J. Xue, E.L.W. Majumder, V.V. Trotter, X. Ge, F.L. Poole II, T.K. Owens, L.M. Lui, T.N. Nielsen, A.P. Arkin, A.M. Deutschbauer, G. Siuzdak, and M.W.W. Adams Deciphering microbial metal toxicity responses using RB-TnSeq and activity-based metabolomics. Applied and Environmental Microbiology 87 (21), e01037-21 (2021). [DOI]: 10.1128/AEM.01037-21] {PMID}:34432491 OSTI:1825256 Deciphering Microbial Metal Toxicity using RB-TnSeq and Activity-Based… Relevant Publication →
Environmental exposure history is critical in groundwater contaminant attenuation - Paradis, CJ, JI Miller, J-W Moon, SJ Spencer, LM Lui, JD Van Nostrand, D Ning, AD Steen, LD McKay, AP Arkin, J Zhou, EJ Alm, TC Hazen Sustained Ability of a Natural Microbial Community to Remove Nitrate from Groundwater (2021) Groundwater [DOI]:10.1111/gwat.13132 OSTI:1807518 A consortium of ENIGMA researchers at University of Tennessee, Oak Ridge National Lab, MIT, Berkeley Lab, University… Relevant Publication →
Microbial Nitrate Removal in a Highly Contaminated Environment is Limited by the Essential Metal Molybdenum - Apr 7, 2021-Molybdenum limitation in the Oak Ridge Reservation contaminated environment, caused by iron and aluminium precipitation, affects nitrate reduction by microorganisms. The Science...The Oak Ridge Reservation (ORR) in Tennessee is a uniquely acidic, high-nitrate- and high-metal-contaminated environment. Although nitrate can be removed by microbes living in this environment, a limited concentration of soluble Molybdenum (Mo) in the ORR reduces… Relevant Publication →
An Integrated Conceptual Microbial Ecology Framework - March 24, 2021-AHolistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. The Science Microbial communities serve critical roles in all ecosystems and have a profound impact on human health, environmental health, and industrial capabilities. As such, it is desirable to have robust, actionable directions for the intervention of microbial community function. However, the multiscale, stochastic, Spatio-temporal and diverse nature… Relevant Publication →
Small is Mighty: Adaptation of Patescibacteria to Groundwater Environment Drives Their Genome Simplicity - Aug 28, 2020-The Science...This new study, by ENIGMA researchers, examined the newly-defined superphylum Patescibacteria, finding that they have developed unique characteristics which help adapt themselves to nutrient-limited but stable conditions in groundwater. Characteristics include highly reduced genome sizes and ultra-small cell size with simplified metabolism pathways for energy and carbon utilization as well as basic systems for DNA replication and… Relevant Publication →