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2. Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

Author

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 Ii, Farris L, 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 WW, Stahl, David A, Elias, Dwayne A, and Hazen, Terry C

Subjects
Hydrology, Earth Sciences, Environmental Sciences, Geochemistry, Geology, Bacteria, Geologic Sediments, Groundwater, Nitrates, Organic Chemicals, Sulfates, Uranium, Water Pollutants, Radioactive, Sediment, Contaminants, Biomass, Meteorology & Atmospheric Sciences
Abstract

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.

Published
2020

4. Draft Genome Sequences of 10 Strains of the Genus Exiguobacterium

Author

Vishnivetskaya, Tatiana A, Chauhan, Archana, Layton, Alice C, Pfiffner, Susan M, Huntemann, Marcel, Copeland, Alex, Chen, Amy, Kyrpides, Nikos C, Markowitz, Victor M, Palaniappan, Krishna, Ivanova, Natalia, Mikhailova, Natalia, Ovchinnikova, Galina, Andersen, Evan W, Pati, Amrita, Stamatis, Dimitrios, Reddy, TBK, Shapiro, Nicole, Nordberg, Henrik P, Cantor, Michael N, Hua, X Susan, and Woyke, Tanja

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Biotechnology, Generic health relevance, Biochemistry and Cell Biology
Abstract

High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to provide insight into their evolutionary strategies for speciation and environmental adaptation. The selected genomes include psychrotrophic and thermophilic species from a range of habitats, which will allow for a comparison of metabolic pathways and stress response genes.

Published
2014

13. Additional file 6 of Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Author

Liang, Renxing, Li, Zhou, Vetter, Maggie C. Y. Lau, Vishnivetskaya, Tatiana A., Zanina, Oksana G., Lloyd, Karen G., Pfiffner, Susan M., Rivkina, Elizaveta M., Wang, Wei, Wiggins, Jessica, Miller, Jennifer, Hettich, Robert L., and Tullis C. Onstott

Abstract

Additional file 6: Table S5. Summary of identified proteins from ancient permafrost at 3.4, 5.8 and 14.8m.

Published
2021
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14. Additional file 9 of Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Author

Liang, Renxing, Li, Zhou, Vetter, Maggie C. Y. Lau, Vishnivetskaya, Tatiana A., Zanina, Oksana G., Lloyd, Karen G., Pfiffner, Susan M., Rivkina, Elizaveta M., Wang, Wei, Wiggins, Jessica, Miller, Jennifer, Hettich, Robert L., and Tullis C. Onstott

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Data_FILES
Abstract

Additional file 9. The scripts used for the analyses in this study.

Published
2021
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15. Additional file of Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Author

Liang, Renxing, Li, Zhou, Vetter, Maggie C. Y. Lau, Vishnivetskaya, Tatiana A., Zanina, Oksana G., Lloyd, Karen G., Pfiffner, Susan M., Rivkina, Elizaveta M., Wang, Wei, Wiggins, Jessica, Miller, Jennifer, Hettich, Robert L., and Tullis C. Onstott

Abstract

Additional file of Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Published
2021
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16. Additional file 2 of Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Author

Liang, Renxing, Li, Zhou, Vetter, Maggie C. Y. Lau, Vishnivetskaya, Tatiana A., Zanina, Oksana G., Lloyd, Karen G., Pfiffner, Susan M., Rivkina, Elizaveta M., Wang, Wei, Wiggins, Jessica, Miller, Jennifer, Hettich, Robert L., and Tullis C. Onstott

Abstract

Additional file 2: Table S1. Statistical summary for MAGs recovered from permafrost sediment samples at 3.4, 5.8 and 14.8 m. Note: CDS refers to protein coding sequence.

Published
2021
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17. Additional file 1 of Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Author

Liang, Renxing, Li, Zhou, Vetter, Maggie C. Y. Lau, Vishnivetskaya, Tatiana A., Zanina, Oksana G., Lloyd, Karen G., Pfiffner, Susan M., Rivkina, Elizaveta M., Wang, Wei, Wiggins, Jessica, Miller, Jennifer, Hettich, Robert L., and Tullis C. Onstott

Abstract

Additional file 1: Figure S1. Geographic location of the sampling site at Cape Chukochii near the East Siberian Sea coast. Figure S2. Image of the drilling site and the schematic of the sediment core (~22 m) from borehole Ch1-17. The red stars indicate the depth of the sediment samples (3.4, 5.8 and 14.8 m, meters below land surface) that were selected for metagenomic sequencing of iDNA and eDNA with and without DNA repair. Figure S3 Temperature and geochemistry profiles of the permafrost sediment collected at various depths from borehole Ch1-17. Figure S4. Concentration of low-molecular-weight organic acids in the permafrost sediment collected at various depths from borehole Ch1-17. Figure S5 Yield of iDNA and eDNA fractions from ancient permafrost sediment at 3.4, 5.8 and 14.8 m. The green bars represent the estimated cell numbers from the intracellular DNA fraction by assuming 2×10-15 g DNA/cell. Figure S6. Size distribution of DNA fragments in iDNA (3.4i, 5.8i and 14.8i) and eDNA (3.4e, 5.8e and 14.8e) fractions from ancient permafrost sediment at 3.4, 5.8 and 14.8 m. The top peaks at 10380 bp for 3.4iDNA and 3.4eDNA sampels were cropped out due to the much higher concentration. Figure S7. Live/Dead cell staining of separated cells from ancient permafrost sediments at 3.4 (top), 5.8 (middle) and 14.8 m (bottom). The green stained live cells by Syto9 are shown in the left panel whereas the red stained dead cells are depicted in the right panel. Figure S8. Relative abundance of MAGs from each metagenome of iDNA and eDNA at 3.4 m with and without PreCR DNA repair. The scale bar indicates the relative abundance of each MAG normalized to the individual sample size as genome copies per million reads. Figure S9. Relative abundance of MAGs from each metagenome of iDNA and eDNA at 5.8 m with and without PreCR DNA repair. The scale bar indicates the relative abundance of each MAG normalized to the individual sample size as genome copies per million reads. Figure S10. Relative abundance of MAGs from each metagenome of iDNA and eDNA at 14.8 m with and without PreCR DNA repair. The scale bar indicates the relative abundance of each MAG normalized to the individual sample size as genome copies per million reads. Figure S11. Percentage of unique reads in each metagenome generated from iDNA and eDNA fractions of the 3.4, 5.8 and 14.8 m samples with and without PreCR DNA repair. Figure S12. Heatmap of the global similarity of each iDNA and eDNA derived metagenomes from the 3.4, 5.8 and 14.8 m samples with and without PreCR DNA repair. The similarity matrix was calculated from the similarity of reads in each metagenome. The scale bar represents the normalized percentage of similarity between two metagenomes with respect to the total number of reads in each metagenome. Figure S13. Principal coordinate analyses (PCoA) of weighted UniFrac distances derived from the microbial community based on the 16S rRNA genes retrieved from each metagenomic dataset of iDNA and eDNA fraction with and without PreCR DNA repair. Figure S14. Number of quality-filtered reads in each metagenome generated from iDNA and eDNA fractions extracted from ancient permafrost sediment at 3.4, 5.8 and 14.8 m with and without PreCR DNA repair. Figure S15. Plot of GC content and contig abundance in each MAG recovered from individual metagenomes of the iDNA and eDNA extracted from the 14.8 m with and without PreCR DNA repair. Figure S16. Groups of carbohydrates active enzymes identified in MAGs recovered from three depths at 3.4, 5.8 and 14.8 m, respectively. The abbreviations for the enzymes classes are as follow: The glycoside hydrolases (GHs), glycosyl transferases (GTs), carbohydrate esterases (CEs) and auxiliary activities (AAs). The relative abundance represents the number of carbohydrates active enzymes identified in each specific subgroup. Figure S17. Relative abundance of proteins identified in the metaproteome from each MAG recovered from the 5.8 m sample. These proteins were involved in carbon and energy metabolism and coping with cold, osmotic and oxidative stresses. The scale bar indicates the balanced spectral counts of proteins. Figure S18. Number of identified proteins in the metaproteomic dataset at 14.8 m when all genes from the metagenome were used as database for search. Figure S19. Number of identified proteins from each MAG recovered from 14.8m. Figure S20 GRiD measurement of bacterial MAGs from the iDNA metagenomic datasets from ancient permafrost sediment at 3.4, 5.8 and 14.8m. The criterion of valid GRiD values (dnaA/ori and ter/dif ratios > 0.8) for each MAGs was selected according to the output results from the GRiD tool.

Published
2021
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21. Desulfotomaculum and methanobacterium spp. dominate a 4- to 5-kilometer-deep fault

Author

Moser, Duane P., Gihring, Thomas M., Brockman, Fred J., Fredrickson, James K., Balkwill, David L., Dollhopf, Michael E., Lollar, Barbara Sherwood, Pratt, Lisa M., Boice, Erik, Southam, Gordon, Wanger, Greg, Baker, Brett J., Pfiffner, Susan M., Li-Hung Lin, and Onstott, T.C.

Subjects
Methanobacteriaceae -- Research, Microbiological chemistry -- Research, Biological sciences
Abstract

Alkaline, sulfidic, 4 to 53 million-year-old meteoric water emanating from a borehole intersecting quartzite-hosted fractures greater than 3.3 kilometer beneath the surface have supported a microbial community dominated by a bacterial species with Desulfotomaculum spp. and an archaeal species related to Methanobacterium spp. These geochemical setting and microbial communities are notably different from microbial ecosystems reported for shallower continental subsurface environments.

Published
2005

23. Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

Author

Moon, Ji-Won, primary, Paradis, Charles J., additional, Joyner, Dominique C., additional, von Netzer, Frederick, additional, Majumder, Erica L., additional, Dixon, Emma R., additional, Podar, Mircea, additional, Ge, Xiaoxuan, additional, Walian, Peter J., additional, Smith, Heidi J., additional, Wu, Xiaoqin, additional, Zane, Grant M., additional, Walker, Kathleen F., additional, Thorgersen, Michael P., additional, Poole II, Farris L., additional, Lui, Lauren M., additional, Adams, Benjamin G., additional, De León, Kara B., additional, Brewer, Sheridan S., additional, Williams, Daniel E., additional, Lowe, Kenneth A., additional, Rodriguez, Miguel, additional, Mehlhorn, Tonia L., additional, Pfiffner, Susan M., additional, Chakraborty, Romy, additional, Arkin, Adam P., additional, Wall, Judy D., additional, Fields, Matthew W., additional, Adams, Michael W.W., additional, Stahl, David A., additional, Elias, Dwayne A., additional, and Hazen, Terry C., additional

Published
2020
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24. Thaumarchaea Genome Sequences from a High Arctic Active Layer

Author

Sun, Emily Wei-Hsin, primary, Hajirezaie, Sassan, additional, Dooner, Mackenzie, additional, Vishnivetskaya, Tatiana A., additional, Layton, Alice, additional, Chauhan, Archana, additional, Pfiffner, Susan M., additional, Whyte, Lyle G., additional, Onstott, Tullis C., additional, and Lau, Maggie C. Y., additional

Published
2020
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28. Integrated characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

Author

Moon, Ji-Won, primary, Paradis, Charles J., additional, Joyner, Dominique C., additional, von Netzer, Frederick, additional, Majumder, Erica L., additional, Dixon, Emma R., additional, Podar, Mircea, additional, Ge, Xiaoxuan, additional, Walian, Peter J., additional, Smith, Heidi J., additional, Wu, Xiaoqin, additional, Zane, Grant M., additional, Walker, Kathleen F., additional, Thorgersen, Michael P., additional, Poole, Farris L., additional, Lui, Lauren M., additional, Adams, Benjamin G., additional, De León, Kara B., additional, Brewer, Sheridan S., additional, Williams, Daniel E., additional, Lowe, Kenneth A., additional, Rodriguez, Miguel, additional, Mehlhorn, Tonia L., additional, Pfiffner, Susan M., additional, Chakraborty, Romy, additional, Arkin, Adam P., additional, Wall, Judy D., additional, Fields, Matthew W., additional, Adams, Michael W. W., additional, Stahl, David A., additional, Elias, Dwayne A., additional, and Hazen, Terry C., additional

Published
2019
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29. Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp

Author

Booker, Anne E., primary, Hoyt, David W., additional, Meulia, Tea, additional, Eder, Elizabeth, additional, Nicora, Carrie D., additional, Purvine, Samuel O., additional, Daly, Rebecca A., additional, Moore, Joseph D., additional, Wunch, Kenneth, additional, Pfiffner, Susan M., additional, Lipton, Mary S., additional, Mouser, Paula J., additional, Wrighton, Kelly C., additional, and Wilkins, Michael J., additional

Published
2019
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35. Sulfur isotope enrichment during maintenance metabolism in the thermophilic sulfate-reducing bacterium Desulfotomaculum putei

Author

Davidson, Mark M., Bisher, M.E., Pratt, Lisa M., Jon Fong, Southam, Gordon, Pfiffner, Susan M., Reches, Z., and Onstott, Tullis C.

Subjects
Electron donor-acceptor complexes -- Analysis, Marine sediments -- Environmental aspects, Sulfate-reducing bacteria -- Genetic aspects, Sulfate-reducing bacteria -- Environmental aspects, Biological sciences
Abstract

The effect of extremely low sulfate reduction rates and electron donor limitation on S isotope fractionation is examined by culturing a thermophilic, sulfate-reducing bacterium, Desulfotomaculum putei, in a biomass-recycling culture vessel (retentostat). The cell-specific rate of sulfate reduction and the specific growth rate have decreased from the exponential phase to the maintenance phase, producing average maintenance coefficients toward the end of the experiments.

Published
2009

39. Metagenomes from Thawing Low-Soil-Organic-Carbon Mineral Cryosols and Permafrost of the Canadian High Arctic

Author

Chauhan, Archana, primary, Layton, Alice C., additional, Vishnivetskaya, Tatiana A., additional, Williams, Daniel, additional, Pfiffner, Susan M., additional, Rekepalli, Bhanu, additional, Stackhouse, Brandon, additional, Lau, Maggie C. Y., additional, Phelps, Tommy J., additional, Mykytczuk, Nadia, additional, Ronholm, Jennifer, additional, Whyte, Lyle, additional, Onstott, Tullis C., additional, and Sayler, Gary S., additional

Published
2014
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41. Draft Genome Sequences of 10 Strains of the Genus Exiguobacterium

Author

Vishnivetskaya, Tatiana A., primary, Chauhan, Archana, additional, Layton, Alice C., additional, Pfiffner, Susan M., additional, Huntemann, Marcel, additional, Copeland, Alex, additional, Chen, Amy, additional, Kyrpides, Nikos C., additional, Markowitz, Victor M., additional, Palaniappan, Krishna, additional, Ivanova, Natalia, additional, Mikhailova, Natalia, additional, Ovchinnikova, Galina, additional, Andersen, Evan W., additional, Pati, Amrita, additional, Stamatis, Dimitrios, additional, Reddy, T. B. K., additional, Shapiro, Nicole, additional, Nordberg, Henrik P., additional, Cantor, Michael N., additional, Hua, X. Susan, additional, and Woyke, Tanja, additional

Published
2014
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42. Trends and future challenges in sampling the deep terrestrial biosphere

Author

Wilkins, Michael J., primary, Daly, Rebecca A., additional, Mouser, Paula J., additional, Trexler, Ryan, additional, Sharma, Shihka, additional, Cole, David R., additional, Wrighton, Kelly C., additional, Biddle, Jennifer F., additional, Denis, Elizabeth H., additional, Fredrickson, Jim K., additional, Kieft, Thomas L., additional, Onstott, Tullis C., additional, Peterson, Lee, additional, Pfiffner, Susan M., additional, Phelps, Tommy J., additional, and Schrenk, Matthew O., additional

Published
2014
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43. Commercial DNA extraction kits impact observed microbial community composition in permafrost samples

Author

Vishnivetskaya, Tatiana A., primary, Layton, Alice C., additional, Lau, Maggie C. Y., additional, Chauhan, Archana, additional, Cheng, Karen R., additional, Meyers, Arthur J., additional, Murphy, Jasity R., additional, Rogers, Alexandra W., additional, Saarunya, Geetha S., additional, Williams, Daniel E., additional, Pfiffner, Susan M., additional, Biggerstaff, John P., additional, Stackhouse, Brandon T., additional, Phelps, Tommy J., additional, Whyte, Lyle, additional, Sayler, Gary S., additional, and Onstott, Tullis C., additional

Published
2013
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45. Microbes in thawing permafrost: the unknown variable in the climate change equation

Author

Graham, David E, primary, Wallenstein, Matthew D, additional, Vishnivetskaya, Tatiana A, additional, Waldrop, Mark P, additional, Phelps, Tommy J, additional, Pfiffner, Susan M, additional, Onstott, Tullis C, additional, Whyte, Lyle G, additional, Rivkina, Elizaveta M, additional, Gilichinsky, David A, additional, Elias, Dwayne A, additional, Mackelprang, Rachel, additional, VerBerkmoes, Nathan C, additional, Hettich, Robert L, additional, Wagner, Dirk, additional, Wullschleger, Stan D, additional, and Jansson, Janet K, additional

Published
2011
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46. Capture of Planktonic Microbial Diversity in Fractures by Long-Term Monitoring of Flowing Boreholes, Evander Basin, South Africa

Author

Davidson, Mark M., primary, Silver, Bianca J., additional, Onstott, T. C., additional, Moser, Duane P., additional, Gihring, Thomas M., additional, Pratt, Lisa M., additional, Boice, Erik A., additional, Lollar, Barbara Sherwood, additional, Lippmann-Pipke, Johanna, additional, Pfiffner, Susan M., additional, Kieft, T. L., additional, Seymore, Walter, additional, and Ralston, Colin, additional

Published
2011
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