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 […]
Subsurface Observatory
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 […]
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 biological denitrification. Two studies now reported the reason why Mo is limited and revealed the mechanisms used by some nitrate-reducing microbes to overcome Mo limitation and survive in these extreme conditions.
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 of microbial processes makes it difficult to achieve predictive understanding of microbial systems, despite the large body of microbial ecology research. To aid efforts that are building predictive understanding from genes to ecosystems, we have developed a conceptual modeling framework (FICSME) that models the composition,
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 translation essential for growth and reproduction. Meanwhile, they lack numerous nonessential functions related to motility, chemotaxis, outer membrane function, polysaccharide metabolism, etc. They also lack CRISPR-mediated phage defense, considered the most important mechanism of bacterial immunity; while possessing alternative strategies for phage resistance.
Setting The Stage For Ongoing Geochemical/Geophysical Characterization of ENIGMA Field Site
May 12, 2020-Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer
Moon, J.-W., Paradis, C.J., Joyner, D.C., von Netzer, F., Majumder, E.L.,Dixon, E.R., Podar, M., Ge, X., Walian, P.J., Smith, H.J., Wu, X., Zane, G.M., Walker, K.F., Thorgersen,M.P., Poole II, , F.L., Lui, L.M., Adams, B.G., De León, K.B., Brewer, S.S., Williams, D.E., Lowe, K.A.,Rodriguez Jr., , M., Mehlhorn, T.L., Pfiffner, S.M., Chakraborty, R., Arkin, A.P., Wall, J.D., Fields, M.W.,Adams, M.W.W., Stahl, D.A., Elias, D.A., Hazen, T.C.
Chemosphere, https://doi.org/10.1016/j.chemosphere.2020.126951
Precisely Quantifying Ecological Processes in Shaping Subsurface Communities
October 20, 2019–ENIGMA researchers at University of Oklahoma have developed a general framework for quantitatively assessing ecological stochasticity. This general framework provides an effective and robust tool to ecologists for quantifying ecological stochasticity. This allows ENIGMA to move towards a more precise quantitative understanding of ecological processes shaping subsurface communities. The new index normalized stochasticity ratio (NST) showed high accuracy and precision (>0.9; >0.3 higher than previous approaches on average). When applied to a groundwater microbial community in response to organic carbon (vegetable oil) injection, NST demonstrated stochasticity increased after injection and decreased when the oil was consumed. By highlighting the caveats, this study also provides guidance for the appropriate use of null model-based approaches for examining community assembly processes.