Browsing by Author "Lui, Lauren M."

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Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer
(Elsevier BV, 2020-05) Moon, Ji-Won; Paradis, Charles J.; Joyner, Dominique C.; von Netzer, Frederick; Majumder, Erica L.; Dixon, Emma R.; Podar, Mircea; Ge, Xiaoxuan; Walian, Peter J.; Smith, Heidi J.; Wu, Xiaoqin; Zane, Grant M.; Walker, Kathleen F.; Thorgersen, Michael P.; Poole, Farris L. II; Lui, Lauren M.; Adams, Benjamin G.; De León, Kara B.; Brewer, Sheridan S.; Williams, Daniel E.; Lowe, Kenneth A.; Rodriguez, Miguel; Mehlhorn, Tonia L.; Pfiffner, Susan M.; Chakraborty, Romy; Arkin, Adam P.; Wall, Judy D.; Fields, Matthew W.; Adams, Michael W.W.; Stahl, David A.; Elias, Dwayne A.; Hazen, Terry C.
The processing of sediment to accurately characterize the spatially-resolved depth proﬁles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, ﬂow rate, and preferential ﬂows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate-and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The ﬂuctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.
Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer
(American Society for Microbiology, 2022-02) Peng, Mu; Wang, Dongyu; Lui, Lauren M.; Nielsen, Torben; Tian, Renmao; Kempher, Megan L.; Tao, Xuanyu; Pan, Chongle; Chakraborty, Romy; Deutschbauer, Adam M.; Thorgersen, Michael P.; Adams, Michael W. W.; Fields, Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Zhou, Aifen; Zhou, Jizhong
Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties.
Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology
(Frontiers Media SA, 2021-03) Lui, Lauren M.; Majumder, Erica L.-W.; Smith, Heidi J.; Carlson, Hans K.; von Netzer, Frederick; Fields, Matthew W.; Stahl, David A.; Zhou, Jizhong; Hazen, Terry C.; Baliga, Nitin S.; Adams, Paul D.; Arkin, Adam P.
Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.