Browsing by Author "Lowe, K. A."

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In situ bioreduction of uranium (VI) in situ and stability of immobilized uranium: Impact of dissolved oxygen
(2007-08) Wu, Wei-Min; Carley, Jack; Luo, Jian; Ginder-Vogel, Matthew A.; Cardenas, Erick; Leigh, Mary Beth; Hwang, Chiachi; Kelly, Shelly D.; Ruan, Chuanmin; Wu, Liyou; Nostrand, Joy V.; Gentry, Terry J.; Lowe, K. A.; Mehlhorn, T. L.; Carroll, Sue L.; Luo, Wensui; Fields, Matthew W.; Gu, Baohua; Watson, David B.; Kemner, K. M.; Marsh, Terence; Tiedje, J. M.; Zhou, Jizhong; Fendorf, Scott; Kitanidis, Peter K.; Jardine, Phil M.; Criddle, Craig S.
Groundwater within Area 3 of the U.S. Department of Energy (DOE) Environmental Remediation Sciences Program (ERSP) Field Research Center at Oak Ridge, TN (ORFRC) contains up to 135 microM uranium as U(VI). Through a series of experiments at a pilot scale test facility, we explored the lower limits of groundwater U(VI) that can be achieved by in-situ biostimulation and the effects of dissolved oxygen on immobilized uranium. Weekly 2-day additions of ethanol over a 2-year period stimulated growth of denitrifying, Fe(III)-reducing, and sulfate-reducing bacteria, and immobilization of uranium as U(IV), with dissolved uranium concentrations decreasing to low levels. Following sulfite addition to remove dissolved oxygen, aqueous U(VI) concentrations fell below the U.S. Environmental Protection Agengy maximum contaminant limit (MCL) for drinking water (< 30/microg L(-1) or 0.126 microM). Under anaerobic conditions, these low concentrations were stable, even in the absence of added ethanol. However, when sulfite additions stopped, and dissolved oxygen (4.0-5.5 mg L(-1)) entered the injection well, spatially variable changes in aqueous U(VI) occurred over a 60 day period, with concentrations increasing rapidly from < 0.13 to 2.0 microM at a multilevel sampling (MLS) well located close to the injection well, but changing little at an MLS well located further away. Resumption of ethanol addition restored reduction of Fe(III), sulfate, and U(VI) within 36 h. After 2 years of ethanol addition, X-ray absorption near-edge structure spectroscopy (XANES) analyses indicated that U(IV) comprised 60-80% of the total uranium in sediment samples. Atthe completion of the project (day 1260), U concentrations in MLS wells were less than 0.1 microM. The microbial community at MLS wells with low U(VI) contained bacteria that are known to reduce uranium, including Desulfovibrio spp. and Geobacter spp., in both sediment and groundwater. The dominant Fe(III)-reducing species were Geothrix spp.
Natural bacterial communities serve as quantitative geochemical biosensors
(2015-03) Smith, Mark B.; Rocha, Andrea M.; Smillie, C. S.; Olesen, S. W.; Paradis, C.; Wu, Liyou; Campbell, J. H.; Fortney, J. L.; Mehlhorn, T. L.; Lowe, K. A.; Earle, J. E.; Phillips, J.; Techtmann, S. M.; Joyner, D. C.; Elias, Dwayne A.; Bailey, K. L.; Hurt, R. A. Jr.; Preheim, S. P.; Sanders, M. C.; Yang, Joy; Mueller, M. A.; Brooks, S.; Watson, David B.; Zhang, Ping; He, Zhili; Dubinsky, E. A.; Adams, P. D.; Arkin, Adam P.; Fields, Matthew W.; Zhou, Jizhong; Alm, E. J.; Hazen, Terry C.
Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. IMPORTANCE Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.