Browsing by Author "Thorgersen, Michael P."

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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.
Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses
(2016-08) Montenegro-Burke, Jose R.; Phommavongsay, Thiery; Aisporna, Aries E.; Huan, Tao; Rinehart, Duane; Forsberg, Erica M.; Poole, Farris L.; Thorgersen, Michael P.; Adams, Michael W. W.; Krantz, Gregory; Fields, Matthew W.; Northen, Trent R.; Robbins, Paul D.; Niedernhofer, Laura J.; Lairson, Luke L.; Benton, H. Paul; Siuzdak, Gary
Active data screening is an integral part of many scientific activities, and mobile technologies have greatly facilitated this process by minimizing the reliance on large hardware instrumentation. In order to meet with the increasingly growing field of metabolomics and heavy workload of data processing, we designed the first remote metabolomic data screening platform for mobile devices. Two mobile applications (apps), XCMS Mobile and METLIN Mobile, facilitate access to XCMS and METLIN, which are the most important components in the computer-based XCMS Online platforms. These mobile apps allow for the visualization and analysis of metabolic data throughout the entire analytical process. Specifically, XCMS Mobile and METLIN Mobile provide the capabilities for remote monitoring of data processing, real time notifications for the data processing, visualization and interactive analysis of processed data (e.g., cloud plots, principle component analysis, box-plots, extracted ion chromatograms, and hierarchical cluster analysis), and database searching for metabolite identification. These apps, available on Apple iOS and Google Android operating systems, allow for the migration of metabolomic research onto mobile devices for better accessibility beyond direct instrument operation. The utility of XCMS Mobile and METLIN Mobile functionalities was developed and is demonstrated here through the metabolomic LC-MS analyses of stem cells, colon cancer, aging, and bacterial metabolism.
Systems biology guided by XCMS Online metabolomics
(2017-04) Huan, Tao; Forsberg, Erica M.; Rinehart, Duane; Johnson, Caroline H.; Ivanisevic, Julijana; Benton, H. Paul; Fang, Mingliang; Aisporna, Aries E.; Hilmers, Brian; Poole, Farris L.; Thorgersen, Michael P.; Adams, Michael W. W.; Krantz, Gregory; Fields, Matthew W.; Robbins, Paul D.; Niedernhofer, Laura J.; Ideker, Trey; Majumder, Erica L.; Wall, Judy D.; Rattray, Nicholas J. W.; Goodacre, Royston; Lairson, Luke L.; Siuzdak, Gary