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Subsurface Biogeochemical Research Program

Significant Scientific Advances and Other Programmatic Activities

SBR and Direct Predecessor Programs (1984-present)

A chronology of significant events related to the Subsurface Biogeochemical Research (SBR) and it's predecessor programs: Environmental Remediation Science Program (ERSP), Natural and Accelerated Bioremediation Research Program (NABIR), and Subsurface Science Program (SSP).

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2017

  • Crunchflow. LBNL Researcher Carl Steefel and his team have been recognized with a R&D100 award for Crunchflow.
  • First report of a methanotrophic bacterium that is capable of taking up and degrading methylmercury via a novel biological pathway. Lu et al., Sci Adv, 2017.Lu, X., W. Gu, L. Zhao, M. Farhan Ul Haque, A.A. DiSpirito, J.D. Semrau, and B. Gu. Methylmercury Uptake and Degradation by Methanotrophs.  Science Advances  3(5) DOI:  10.1126/sciadv.1700041
  • First demonstration that Archaea have CRISPR-Cas9 systems. Burstein et al., Nature Comm, 2017. Burstein, D., Sun, C.L., Brown, C.T., Sharon, I., Anantharaman, K., Probst, A.J, Thomas, B.C., and Banfield, J.F. Major bacterial lineages are essentially devoid of CRISPR-Cas viral defense systems.  Nature Communications  7:10613 DOI:  10.1038/ncomms10613 See this BER Highlight for more.
  • Demonstrated that when metal-laden (e.g., Pb, As) mine wastes become buried in stream sediments, such as from the Gold King Mine spill into the Animas River in Colorado, anaerobic microorganisms are likely to drive the remobilization of these metals into the stream over the long term. Saup et al., Env Sci Proc & Impacts, 2017.Saup, Casey M., Kenneth H. Williams, Lucía Rodríguez-Freire, José M. Cerrato, Michael D. Johnston, and Michael J. Wilkins. Anoxia Stimulates Microbially Catalyzed Metal Release from Animas River Sediments.  Environmental Science: Processes and Impacts  19:578-585 DOI:  10.1039/C7EM00036G
  • Selection (Feb 2017) of IDEAS-ECP, a new Exascale Computing Project (ECP) to help software development teams increase the quality of their products by establishing a hub/portal for software development. Multi-lab effort that includes most collaborators from the IDEAS project that SBR managers started in 2014.
  • Incorporation of microbially-driven biogeochemical processes into the eSTOMP, a parallelized reactive transport code to simulate understanding of biogeochemical cycling and water table dynamics in a variably saturated floodplain at the Rifle, CO site. Yabusaki et al., Env Sci Technol, 2017.Yabusaki, Steven B., Michael J. Wilkins, Yilin Fang, Kenneth H. Williams, Bhavna Arora, John Bargar, Harry R. Beller, Nicholas J. Bouskill, Eoin L. Brodie, John N. Christensen, Mark E. Conrad, Robert E. Danczak, Eric King, Mohamad R. Soltanian, Nicolas F. Spycher, Carl I. Steefel, Tetsu K. Tokunaga , Roelof Versteeg, Scott R. Waichler, and Haruko M. Wainwright. Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.  Environmental Science & Technology  51(6):3307-3317 DOI:  10.1021/acs.est.6b04873

2016

  • Demonstrated that metabolic handoffs among microbial community members is critical for cycling nutrients. Anantharaman et al., Nature Comm, 2016.Anantharaman, Karthik, Christopher T. Brown, Laura A. Hug, Itai Sharon, Cindy J. Castelle, Alexander J. Probst, Brian C. Thomas, Andrea Singh, Michael J. Wilkins, Ulas Karaoz, Eoin L. Brodie, Kenneth H. Williams, Susan S. Hubbard, and Jillian F. Banfield. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.  Nat Commun  7 DOI:  10.1038/ncomms13219 See this BER Highlight and Berkeley Lab News article for more.
  • Selection (Fall 2016) of “An Exascale Subsurface Simulator of Coupled Flow, Transport, Reactions and Mechanics,” a new Exascale Computing Project (ECP) to advance the incorporation of fluid flow and reactive chemical processes into the Chombo-Crunch (parallelized) reactive transport code.
  • Selection (Fall 2016) of xSDK4ECP, a new Exascale Computing Project (ECP) to develop community policies and interoperability layers among numerical reactive transport codes/packages, especially ones used by the SBR research community (e.g., PFLOTRAN, Alquimia), and several relevant numerical libraries. Multi-lab effort that includes most collaborators from the IDEAS project that SBR managers started in 2014.
  • Demonstrated that lateral groundwater flow controls evapotranspiration on a Continental/regional scale using the parallelized ParFlow reactive transport code on an HPC system. Maxwell and Condon, Science, 2016.Maxwell, R.M., and L.E. Condon. Connections between Groundwater Flow and Transpiration Partitioning.  Science  353(6297):377-380 DOI:  10.1126/science.aaf7891 See   BER highlight for more.
  • Significantly expanded the “Tree of Life.”   Hug et al., Nature Micro, 2016.Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D.A., Finstad, K.M., Amundson, R., Thomas, B.C., and Banfield, J.F.. A new view of the tree of life.  Nature Microbiology  in press DOI:  10.1038/NMICROBIOL.2016.48
  • Developed E4D-RT, a real-time 4D subsurface imaging technology that received a 2016 R&D 100 award.  See this news item for more details and this YouTube video for an explanation of the technology.
  • Demonstrated that groundwater-surface water mixing under variable river discharge conditions, which are driven by the water release patterns of a major upstream dam, drives dynamic coupling between biogeochemistry and microbial ecology in the hyporheic zone. Stegen et al., Nature Comm, 2016.Stegen, J. C., J. K. Fredrickson, M. J. Wilkins, A. E. Konopka, W. C. Nelson, E. V. Arntzen, W. B. Chrisler, R. K. Chu, R. E. Danczak, S. J. Fansler, D. W. Kennedy, C. T. Resch, and M. M. Tfaily. Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.  Nature Communications  7:11237 DOI:  10.1038/ncomms11237 See this YouTube video for more details.
  • Demonstrated that fluctuating levels of river water, caused by upriver dam operations, drives the release of uranium from subsurface sediments adjacent to the river. Incorporated 3 years of data associated with a Hanford Site uranium plume that borders the Columbia River into the parallelized PFLOTRAN reactive transport code. Zachara et al., Water Res Res, 2016.Zachara, J., X. Chen, C. Murray, and G. E. Hammond. River stage influences on uranium transport in a hydrologically dynamic groundwater-surface water transition zone.  Water Resources Research  52 DOI:  10.1002/2015WR018009
  • Publication of Deep Life: The Hunt for the Hidden Biology of Earth, Mars and Beyond, by former BER-funded principal investigator, T.C. Onstott. 2016. Princeton University Press. The first part of the book describes research conducted by investigators funded by BER from 1985-1996.

2015

  • Found mercury methylation genes in all known mercury methylating bacteria from a wide variety of environments. Podar et al., Sci Adv, 2015.Podar, Mircea, Cynthia C. Gilmour, Craig C. Brandt, Allyson Soren, Steven D. Brown, Bryan R. Crable, Anthony V. Palumbo, Anil C. Somenahally and Dwayne A. Elias. Global prevalence and distribution of genes and microorganisms involved in mercury methylation.  Science Advances  1(9):e1500675 DOI:  10.1126/sciadv.1500675
  • Identified completely functional nanobacterial-sized cells from groundwater at the Rifle, CO UMTRA Site, and thereby pinpointed the lower size limit possible for microbial life. Luef et al., Nature Comm, 2015.Luef, B., K. R. Frischkorn, K. C. Wrighton, H.-Y. N. Holman, G. Birarda, B. C. Thomas, A. Singh, K. H. Williams, C. E. Siegerist, S. G. Tringe, K. H. Downing, L. R. Comolli, and J. F. Banfield. Diverse uncultured ultra-small bacterial cells in groundwater.  Nature Communications  6 DOI:  10.1038/ncomms7372 For more details see this Berkeley Lab News article.  
  • Summary publication by multiple authors that describes a dozen different reactive transport codes, several of which were advanced with BER funding. Steefel et al., Compu Geosci, 2015.Steefel, C. I., C. A. J. Appelo, B. Arora, D. Jacques, T. Kalbacher, O. Kolditz, V. Lagneau, P. C. Lichtner, K. U. Mayer, J. C. L. Meeussen, S. Molins, D. Moulton, H. Shao, J. Simunek, N. Spycher, S. B. Yabusaki, G. T. Yeh. Reactive transport codes for subsurface environmental simulation.  Computational Geosciences  19(3):445-478 DOI:  10.1007/s10596-014-9443-x

2014

  • BER managers, in partnership with the Office of Advanced Scientific Computing Research (ASCR), establish the Interoperable Design of Extreme Scale Application Software (IDEAS) project to promote an integrated and interoperable software ecosystem of HPC codes and libraries. BER program managers establish three use cases to motivate the research efforts:   1) hydro-biogeochemical cycling in the upper Colorado River system, 2) hydrology and carbon dynamics of the Arctic tundra, and 3) hydrologic, land surface and atmospheric coupling over the continental U.S. IDEAS Project website.
  • Two mechanistic HPC modeling studies demonstrate molecular through watershed controls on long-term uranium and iodine plume behavior. Chang et al., J Environ Chem Eng, 2014Chang, H.-S., C. Xu, K. A. Schwehr, S. Zhang, D. I. Kaplan, J. C. Seaman, C. Yeager, and P. H. Santschi. Model of Radioiodine Speciation and Partitioning in Organic-rich and Organic-poor Soils from the Savannah River Site.  Journal of Environmental Chemical Engineering  2:1321-1330 DOI:  10.1016/j.jece.2014.03.009; Kaplan et al., Crit Rev Env Sci & Tech, 2014.Kaplan, D. I., M. E. Denham, S. Zhang, C. Yeager, C. Xu, K. A. Schwehr, H. P. Li, Y. F. Ho, D. Wellman, and P. H. Santschi. Radioiodine Biogeochemistry and Prevalence in Groundwater.  Critical Reviews of Environmental Science & Technology 44(20):2287-2335 DOI: 10.1080/10643389.2013.828273
  • Demonstrated the feasibility of reducing technetium transport in groundwater by reacting technetium with zero-valent iron to form technetium sulfide. Fan et al., Env Sci Technol, 2014.Fan, D., R.P. Anitori, B.M. Tebo, P.G. Tratnyek, J.S. Lezama Pacheco, R.K. Kukkadapu, L. Kovarik, M.H. Engelhard, and M.E. Bowden. Oxidative Remobilization of Technetium Sequestered by Sulfide-Transformed Nano Zero-valent Iron.  Environmental Science & Technology  48(13):7409-7417 DOI:  10.1021/es501607s   See   EMSL News article for more.
  • First proteomic study of microbial communities from groundwater from the Rifle, CO UMTRA Site. Wrighton et al., ISME J, 2014.Wrighton, K. C., C. J. Castelle, M.J. Wilkins, L. A. Hug, I. Sharon, B. C. Thomas, K. M. Handley, S. Mullin, C. D. Nicora, A. Singh, M. S. Lipton, P. E. Long, K. H. Williams, and J. F. Banfield. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer.  ISME J  8(7):1452-63 DOI:  10.1038/ismej.2013.249
  • Discovered that in alkaline aquifers, some bacteria can use elemental sulfur to indirectly reduce iron, which can then indirectly affect contaminant mobility in the subsurface. See this highlight for more details. Flynn et al., Science, 2014Flynn, T. M., E. J. O’Loughlin, B. Mishra, T. J. DiChristina, and K. M. Kemner. Sulfur-mediated electron shuttling during bacterial iron reduction.  Science  344(6187):1039-1042 DOI:  10.1126/science.1252066; Friedrich and Finster, Science, 2014Friedrich, M. W., and K. W. Finster. How Sulfur Beats Iron.  Science  344:974-75 DOI:  10.1126/science.1255442
  • Multiple studies provide fundamental understanding of plutonium hydro-biogeochemistry in the Hanford Site subsurface. Enables DOE Office of Environmental Management (EM) to make decisions concerning long-term stewardship of contaminated groundwater and soils at the Hanford Site. Xu et al., Env Sci Technol, 2014Xu, C., M. Athon, Y.-F. Ho, H.-S. Chang, S. Zhang, D. I. Kaplan, K. A. Schwehr, N. DiDonato, P. G. Hatcher, and P. H. Santschi. Plutonium Immobilization and Re-mobilization by Soil Mineral and Organic Matter in the Far-field of the Savannah River Site, USA.  Environmental Science & Technology  48(6):3186-3195 DOI:  10.1021/es404951y; Xu et al., Env Sci Technol, 2015Xu, Chen, Saijin Zhang, Daniel I. Kaplan, Yi-Fang Ho, Kathleen A. Schwehr, Kimberly A. Roberts, Hongmei Chen, Nicole DiDonato, Matthew Athon, Patrick G. Hatcher, and Peter H. Santschi. Evidence for Hydroxamate Siderophores and Other N-Containing Organic Compounds Controlling  239,240Pu Immobilization and Remobilization in a Wetland Sediment.  Environmental Science & Technology  49(19):11458-11467 DOI:  10.1021/acs.est.5b02310; DiDonato et al., Env Sci Technol, 2017DiDonato, Nicole, Chen Xu, Peter H. Santschi, and Patrick G. Hatcher. Sub-Structural Components of Organic Colloids from a Pu-Polluted Soil with Implications for Pu Mobilization.  Environmental Science & Technology  DOI:  10.1021/acs.est.6b04955; Lin et al., Env Sci Technol 2017.Lin et al., Environmental Science & Technology 2017
  • Two studies provide fundamental understanding of plutonium and neptunium hydrobiogeochemistry in the Nevada National Security Site (NNSS) subsurface. Enables NNSA to make decisions concerning long-term stewardship of contaminated groundwater and soils at NNSS (formerly the Nevada Test Site). Zhao et al., J Env Radioact, 2014Zhao, P., R. M. Tinnacher, M. Zavarin, and A. B. Kersting. Analysis of Trace Neptunium in the Vicinity of Underground Nuclear Tests at the Nevada National Security Site.  J Environ. Radioact  137:163-172 DOI:  10.1016/j.jenvrad.2014.07.011; Kersting, Inorganic Chemistry, 2013Kersting, A.B. Plutonium transport in the environment. Invited.  Inorganic Chemistry  52:3533-3546 DOI:  10.1021/ic3018908.

2013

  • Multiple studies enhance scientific understanding of the importance of spatial heterogeneities in subsurface environments for influencing the types and rates of geochemical reactions. Liu et al., Env Sci Technol, 2013Liu et al., Environmental Science & Technology, 2013; Salehikhoo and Li, Geochim Cosmochim Acta, 2015Salehikhoo, F. and L. Li. The role of mineral spatial patterns in determining magnesite dissolution rates: When does it matter?.  Geochimica et Cosmochimica Acta  155:107-121 DOI:  10.1016/j.gca.2015.01.035; Zachara et al., Env Sci Technol, 2016Zachara JM, Brantley SL, Chorover JD, Ewing RP, Kerisit SN, Liu C, Perfect E, Rother G and Stack AG. Internal domains of natural porous media revealed: Critical locations for transport, storage, and chemical reaction.  Environmental Science & Technology 50:2811-2829 DOI:  10.1021/acs.est.5b05015; Wang and Li, Env Sci Technol, 2016Wang, Yuwei, Jeffra K. Schaefer, Bhoopesh Mishra, and Nathan Yee. Intracellular Hg(0) Oxidation in  Desulfovibrio desulfuricansND132.  Environmental Science & Technology  50(20):11049-11056 DOI:  10.1021/acs.est.6b03299.
  • Multiple microbial, contaminant mobility, and geophysical studies demonstrate the importance of “hot spots” and “hot moments” in controlling fluxes of key elements (e.g., C, Fe, etc.) and contaminant transformations at field-relevant scales. Hug et al., Microbiome, 2013Hug, L. A., C. J. Castelle, K. C. Wrighton, B. C. Thomas, I. Sharon, K. R. Frischkorn, K. H. Williams, S. G. Tringe, and J. F. Banfield. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling.  Microbiome  1:22 DOI:  10.1186/2049-2618-1-22; Lee et al., Geochim Cosmochim Acta, 2014Lee, J.-H., J. M. Zachara, J. K. Fredrickson, S. M. Heald, J. P. McKinley, A. E. Plymale, C. T. Resch, and D. A. Moore. Fe(II)- and sulfide-facilitated reduction of  99Tc(VII)O4-  in microbially reduced hyporheic zone sediments.  Geochimica et Cosmochimica Acta 136:247-264 DOI:  10.1016/j.gca.2013.08.017; Hug et al., Env Micro, 2016Hug, L.A., Thomas, B.C. Sharon, I., Brown, C.T., Sharma, R., Hettich, R.L., Wilkins, M.J., Williams, K.H., Singh, A. and Banfield, J.F. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.  Environmental Microbiology  18:159-173 DOI:  10.1111/1462-2920.12930; Bao et al., Env Sci Technol, 2016Bao et al., Env Sci Technol, 2016; Janot et al., Env Sci Technol, 2016Janot, N., J. S. Lezama Pacheco, D. Q. Pham, T. M. O'Brien, D. Hausladen, V. Noel, F. Lallier, K. Maher, S. Fendorf, K. H. Williams, P. E. Long, and J. R. Bargar. Physico-Chemical Heterogeneity of Organic-Rich Sediments in the Rifle Aquifer, CO: Impact on Uranium Biogeochemistry.  Environmental Science & Technology  50(1):46-53 DOI:  10.1021/acs.est.5b03208 ; Jewell et al, ISME J, 2016Jewell, T. N. M., U. Karaoz, E. L. Brodie, K. H. Williams, and H. R. Beller. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer.  ISME J  DOI:  10.1038/ismej.2016.25; Tokunaga et al., Vadose Zone J, 2016Tokunaga, T. K., Y. Kim, M. E. Conrad, M. Bill, C. Hobson, K. H. Williams, W. Dong, J. Wan, M. J. Robbins, P. E. Long, B. Faybishenko, J. N. Christensen, and S. S. Hubbard. Deep vadose zone respiration contributions to carbon dioxide fluxes from a semiarid floodplain.  Vadose Zone Journal  15(7):1-14 DOI:  10.2136/vzj2016.02.0014; Arora et al., Biogeochemistry, 2016Arora, B., N. F. Spycher, C. I. Steefel, S. Molins, M. Bill, M. E. Conrad, W. Dong, B. Faybishenko, T. K. Tokunaga, J. Wan, K. H. Williams, and S. B. Yabusaki. Influence of Hydrological, Biogeochemical and Temperature Transients on Subsurface Carbon Fluxes in a Flood Plain Environment.  Biogeochemistry  127(2):367-396 DOI:  10.1007/s10533-016-0186-8; Wainwright et al., Water Res Res, 2016Wainwright, H. M., A. Flores Orozco, M. Bücker, B. Dafflon, J. Chen, S. S. Hubbard, and K. H. Williams. Hierarchical Bayesian method for mapping biogeochemical hot spots using induced polarization imaging.  Water Resour. Res.  52 DOI:  10.1002/2015WR017763; Yabusaki et al, Env Sci Technol, 2017Yabusaki, Steven B., Michael J. Wilkins, Yilin Fang, Kenneth H. Williams, Bhavna Arora, John Bargar, Harry R. Beller, Nicholas J. Bouskill, Eoin L. Brodie, John N. Christensen, Mark E. Conrad, Robert E. Danczak, Eric King, Mohamad R. Soltanian, Nicolas F. Spycher, Carl I. Steefel, Tetsu K. Tokunaga , Roelof Versteeg, Scott R. Waichler, and Haruko M. Wainwright. Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.  Environmental Science & Technology  51(6):3307-3317 DOI:  10.1021/acs.est.6b04873; Jewell et al., Front Microbiol, 2017Jewell, T. N. M., U. Karaoz, M. Bill, R. Chakraborty, E. L. Brodie, K. H. Williams, and H. R. Beller. Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer.  Frontiers in Microbiology 8(40) DOI:  10.3389/fmicb.2017.00040.
  • Modeling results prove to be the key for discovering the genetic basis (i.e., the genes) for mercury methylation. Parks et al, Science, 2013.Parks, J. M., A. Johs, M. Podar, R. Bridou, R. A. Hurt Jr., S. D. Smith, S. J. Tomanicek, Y. Qian, S. D. Brown, C. C. Brandt, A. V. Palumbo, J. C. Smith, J. D. Wall, D. A. Elias, and L. Liang. The genetic basis for bacterial mercury methylation.  Science  339:1332-1335 DOI:  10.1126/science.1230667 See this BER highlight for more details.
  • Demonstrated the great metabolic diversity of the microbiome of subsurface sediments through the use of genomic sequencing. Castelle et al., Nature, 2013.Castelle, C. J., L. A. Hug, K. C. Wrighton, B. C. Thomas, K. H. Williams, D. Wu, S. G. Tringe, S. W. Singer, J. A. Eisen, and J. F. Banfield. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.  Nature Commun  DOI:  10.1038/ncomms3120
  • Discovered that multiple species of bacteria convert elemental mercury to toxic methylmercury. See this BER highlight for more details.
  • Field-based demonstration that used proteomic analyses to identify active metabolic pathways. Gihring et al., Appl Env Microbiol, 2011Gihring, T. M., G. X. Zhang, C. C. Brandt, S. C. Brooks, J. H. Campbell, S. Carroll, C. S. Criddle, S. J. Green, P. Jardine, J. E. Kostka, K. Lowe, T. L. Mehlhorn, W. Overholt, D. B. Watson, Z. M. Yang, W. M. Wu, and C. W. Schadt. A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer.  Applied And Environmental Microbiology  77:5955-5965 DOI: 10.1128/AEM.00220-11; Chourey et al., Proteomics, 2013Chourey, K., S. Nissen, T. Vishnivetskaya, M. Shah, S. Pfiffner, R. L. Hettich, and F. E. Loeffler. Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site.  Proteomics  13:2921-2930 DOI:  10.1002/pmic.201300155.
  • Demonstrated that proteins in the cell wall of some bacteria produce an electric current when in contact with a mineral surface, thereby allowing the bacteria to “breathe” the iron in the mineral. See EMSL News for more details.

2012

  • Identified uncultivatable bacteria from the subsurface using metagenomics approaches and determined their roles in modulating subsurface biogeochemical processes.   Wrighton et al., Science, 2012.Wrighton, K. C., B. C. Thomas, I. Sharon, C. S. Miller, C. J. Castelle, N. C. VerBerkmoes, M. J. Wilkins, R. L. Hettich, M. S. Lipton, K. H. Williams, P. E. Long, and J. F. Banfield. Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla.  Science  337:1661-1665 See   EMSL News article for more.
  • Discovery of novel nitrate-reducing bacteria from the subsurface. Subsequent studies change the conceptual model of nitrogen cycling. Green et al., Appl Environ Microbiol, 2012Green, S. J., O. Prakash, P. Jasrotia, W. A. Overholt, E. Cardenas, D. Hubbard, J. M. Tiedje, D. B. Watson, C. W. Schadt, S. C. Brooks, and J. E. Kostka. Denitrifying Bacteria from the Genus  Rhodanobacter  Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site.  Applied and Environmental Microbiology  78:1039-1047 DOI:  10.1128/AEM.06435-11; Kostka et al., J Bacteriol, 2012Kostka, J. E., S. J. Green, L. Rishishwar, O. Prakash, L. S. Katz, L. Marino-Ramirez, I. K. Jordan, C. Munk, N. Ivanova, N. Mikhailova, D. B. Watson, S. D. Brown, A. V. Palumbo, and S. C. Brooks. Genome Sequences for Six  Rhodanobacter  Strains, Isolated from Soils and the Terrestrial Subsurface, with Variable Denitrification Capabilities.  Journal of Bacteriology  194:4461-4462 DOI:  10.1128/JB.00871-12; Prakash et al., Int J Syst Evol Microbiol, 2012Prakash, O., S. J. Green, P. Jasrotia, W. A. Overholt, A. Canion, D. B. Watson, S. C. Brooks, and J. E. Kostka.  Rhodanobacter denitrificans  sp. nov., isolated from nitrate-rich zones of a contaminated aquifer.  International Journal of Systematic and Evolutionary Microbiology  DOI:  10.1099/ijs.0.035840-0; Venkatramanan et al., Genome Ann, 2013Venkatramanan et al., Genome Ann, 2013
  • Developed new approach to model the chemical interactions of plutonium with minerals and biological molecules using density functional theory. Huang et al., Chem Phys Lett, 2012.Huang, P., M. Zavarin, and A. B. Kersting.  Ab initio  structure and energetics of Pu(OH)4  and Pu(OH)4(H2O)n clusters: Comparison between density functional and multi-reference theories.  Chemical Physics Letters  543:193-198 DOI:  10.1016/j.cplett.2012.06.033 .   See this BER highlight for more details.
  • Multiple studies demonstrate that microorganisms are involved in the speciation and cycling of iodine. Li et al., App Env Micro, 2011Li, H.P., R. Brinkmeyer, W. L. Jones, S. Zhang, C. Xu, K. A. Schwehr, P. H. Santschi, D. I. Kaplan, and C. M. Yeager. Iodide Accumulation by Aerobic Bacteria Isolated from Subsurface Sediments of a  129I-Contaminated Aquifer at the Savannah River Site, South Carolina.  Applied And Environmental Microbiology  77(6):2153-2160 DOI:  10.1128/AEM.02164-10; Li et al., Env Poll Tox, 2012Li, H.-P., R. Brinkmeyer, W. L. Jones, S. Zhang, C. Xu, Y.-F. Ho, K. A. Schwehr, D. I. Kaplan, P. H. Santschi, and C. M. Yeager. Iodide Oxidizing Activity of Bacteria from Subsurface Sediments of the Savannah River Site, SC, USA.  Interdisciplinary Studies on Environmental Chemistry Vol. 6 - Environmental Pollution and Ecotoxicology. M. Kawaguchi, K. Misaki, H. Sato, T. Yokokawa, T. Itai, T. M. Nguyen, J. Ono, and S. Tanabe (ed.), Terra Scientific Publishing Company Tokyo 89-97; Li, et al., 10.1021/es203683v, 2012 Li, H.-P., C. M. Yeager, R. Brinkmeyer, S. Zhang, Y.-F. Ho, C. Xu, W. L. Jones, K. A. Schwehr, S. Otosaka, D. I. Kaplan, and P. H. Santschi. Organic acids produced by subsurface bacteria enhance iodide oxidation in the presence of hydrogen peroxide.  Environmental Science & Technology  46:4837-4844 DOI:  10.1021/es203683v; Li et al., App Env Micro, 2014Li, H.-P., B. Daniel, D. Creeley, R. Grandbois, S. Zhang, C. Xu, Y.-F. Ho, K. A. Schwehr, D. I. Kaplan, P. H. Santschi, C. Hansel, and C. M. Yeager. Superoxide production by a manganese-oxidizing bacterium facilitates iodide oxidation.  Applied and Environmental Microbiology  80(9):2693-2699 DOI:  10.1128/AEM.00400-14 ; Grandbois et al., Geomicrobiology, 2017Grandbois, R., C.M. Yeager, Y. Tani, C. Xu,, S. Zhang, M. Beaver, K.A. Schwehr, D.I. Kaplan, and P.H. Santschi. Biogenic manganese oxides facilitate iodide oxidation at pH ≤ 5.  Geomicrobiology  DOI:  10.1080/01490451.2017.1338795.

2011

  • Field-based experiments, and subsequent genome-informed reactive transport model simulations, demonstrate that the effect of slow-release carbon amendments for coupling microbially-driven dynamics with geochemical feedbacks in aquifers can be used to immobilize uranium. Gihring et al, Appl Env Microbiol, 2011Gihring, T. M., G. X. Zhang, C. C. Brandt, S. C. Brooks, J. H. Campbell, S. Carroll, C. S. Criddle, S. J. Green, P. Jardine, J. E. Kostka, K. Lowe, T. L. Mehlhorn, W. Overholt, D. B. Watson, Z. M. Yang, W. M. Wu, and C. W. Schadt. A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer.  Applied And Environmental Microbiology  77:5955-5965 DOI:  10.1128/AEM.00220-11; Watson et al., Env Sci Technol, 2013Watson, D. B., Wu, W.-M., T. Mehlhorn, Tang, G., J. Earles, Lowe, K., T. M. Gihring, G. Zhang, J. Phillips, M. I. Boyanov, B. P. Spalding, C. Schadt, K. M. Kemner, C. S. Criddle, P. M. Jardine, and S. C. Brooks. In situ bioremediation of uranium with emulsified vegetable oil as the electron donor.  Environmental Science & Technology  47(12):6440-6448 DOI:  10.1021/es3033555; Tang et al., Env Sci Technol, 2013Tang et al., Environmental Science & Technology, 2013; Tang et al., Env Sci Technol, 2013Tang et al., Environmental Science & Technology, 2013.
  • Multiple studies demonstrate that iodine is less mobile and plutonium is more mobile than current models predict (based on I and Pu transport studies at Savannah River, Hanford, and Fukushima). Zhang et al., Env Sci Technol, 2010Zhang, S., K. A. Schwehr, Y. F. Ho, C. Xu, K. A. Roberts, D. I. Kaplan, R. Brinkmeyer, C. M. Yeager, and P. H. Santschi. A Novel Approach for the Simultaneous Determination of Iodide, Iodate and Organo-Iodide for I-127 and I-129 in Environmental Samples Using Gas Chromatography-Mass Spectrometry.  Environmental Science & Technology  44:9042-9048 DOI:  10.1021/es102047y; Kaplan et al., Env Sci Technol, 2011Kaplan, D. I., K. A. Roberts, K. A. Schwehr, M. S. Lilley, R. Brinkmeyer, M. E. Denham, D. Diprete, H. P. Li, B. A. Powell, C. Xu, C. M. Yeager, S. J. Zhang, and P. H. Santschi. Evaluation of a Radioiodine Plume Increasing in Concentration at the Savannah River Site.  Environmental Science & Technology  45:489-495 DOI:  10.1021/es103314n; Xu et al., Env Sci Technol, 2011Xu, C.; Miller, E.J.; Zhang, S., Li, H.-P.; Ho, Y.-F.; Schwehr, K.A.; Kaplan, D.L.; Otosaka, S.; Roberts, K.A.; Brinkmeyer, R.; Yeager, C.M.; and Santschi, P.H.. Sequestration and remobilization of radioiodine (129I) by soil organic matter and possible consequences of the remedial action at the Savannah River Site.  Environmental Science & Technology  45(23):9975-9983 DOI:  10.1021/es201343d; Otosaka et al., Sci Total Env 2011Otosaka, S., K. A. Schwehr, D. I. Kaplan, K. A. Roberts, S. Zhang, C. Xu, H.-P. Li, Y.-F. Ho, R. Brinkmeyer, C. M. Yeager, and P. H. Santschi. Factors controlling mobility of  127I and  129I species in an acidic groundwater plume at the Savannah River Site.  Science Of The Total Environment  409:3857-3865 DOI:  10.1016/j.scitotenv.2011.05.018; Chang et al., J Env Chem Eng, 2013Chang et al., J Env Chem Eng, 2013; Santschi et al., App Geochem, 2016Santschi, P.H., C. Xu, S. Zhang, K.A. Schwehr, R. Grandbois, D. Kaplan, and C. Yeager. Iodine and Plutonium Association with Natural Organic Matter: A Review of Recent Advances.  Applied Geochemistry  in press DOI:  10.1016/j.apgeochem.2016.11.009; Xu et al., J Env Radioactiv, 2016Xu, C., S. Zhang, Y. Sugiyama, N. Ohte, Y.-F. Ho, N. Fujitake, D.I. Kaplan, C.M. Yeager, K.A. Schwehr, and P.H. Santschi. Role of natural organic matter on iodine and (239)(,240)Pu distribution and mobility in environmental samples from the northwestern Fukushima Prefecture, Japan.  Journal of Environmental Radioactivity  153:156-166 DOI:  10.1016/j.jenvrad.2015.12.022.
  • First effort to model the interactions of uranium with aluminum oxide, a common soil mineral. See this highlight for more details.

2010

  • BER transitions the ERSP into the Subsurface Biogeochemical Research (SBR) program.
  • Studies provide the basis for analytical developments that enable scientists to speciate iodine.   Zhang et al., Env Sci Technol, 2010Zhang, S., K. A. Schwehr, Y. F. Ho, C. Xu, K. A. Roberts, D. I. Kaplan, R. Brinkmeyer, C. M. Yeager, and P. H. Santschi. A Novel Approach for the Simultaneous Determination of Iodide, Iodate and Organo-Iodide for I-127 and I-129 in Environmental Samples Using Gas Chromatography-Mass Spectrometry.  Environmental Science & Technology  44:9042-9048 DOI:  10.1021/es102047y; Schwehr et al., Sci Total Env, 2014.Schwehr, K. A., S. Otosaka, S. Merchel, D. I. Kaplan, S. Zhang, C. Xu, H.-P. Li, Y.-F. Ho, C. M. Yeager, P. H. Santschi, and ASTER Team. Speciation of iodine isotopes inside and outside of a contaminant plume at the Savannah River Site.  Science of the Total Environment  497-498:671-678 DOI:  10.1016/j.scitotenv.2014.07.006

2009

  • Discovered that uranium can exist in the pentavalent oxidation state - U(V) in nature. Ilton et al., Env Sci Technol, 2009.Ilton, E. S., J. F. Boily, E. C. Buck, F. N. Skomurski, K. M. Rosso, C. L. Cahill, J. R. Bargar, and A. R. Felmy. Influence of Dynamical Conditions on the Reduction of U-VI at the Magnetite-Solution Interface.  Environmental Science & Technology  44:170-176 DOI:  10.1021/es9014597   See   EMSL News article for more.
  • Developed the first subsurface reactive transport models to be directly informed by genome-scale models of microbial metabolism. Scheibe et al., Microb Biotech, 2009Scheibe, T.D., R. Mahadevan, Y. Fang, S. Garg, P.E. Long, and D.R. Lovley. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.  Microbial Biotechnology  2(2):274-286 DOI:  10.1111/j.1751-7915.2009.00087.x; Fang et al. Appl Env Micro, 2012Fang, Y. L., M. J. Wilkins, S. B. Yabusaki, M. S. Lipton, and P. E. Long. Evaluation of a Genome-Scale  In Silico  Metabolic Model for  Geobacter metallireducens  by Using Proteomic Data from a Field Biostimulation Experiment.  Applied and Environmental Microbiology  78:8735-8742 DOI:  10.1128/AEM.01795-12; Tartakovsky et al., Adv Water Resour, 2013Tartakovsky, G. D., A. M. Tartakovsky, T. D. Scheibe, Y. Fang, R. Mahadevan, and D. R. Lovley. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport.  Advances in Water Resources 59:256-270 DOI:  10.1016/j.advwatres.2013.05.007.

2008

  • BER managers establish Scientific Focus Area (SFA) programs at the DOE National Labs. SFAs are expected to be long-term strategic investments that are structured to be team-oriented efforts, make use of laboratory capabilities (including user facilities), aligned with the directions of BER research programs, and subject to peer review every three years.
  • Discovered that colloids facilitate the transport of radionuclides in groundwater (especially Pu). Although not published until after the closure of Rocky Flats, this work contributed to the regulatory decision to close Rocky Flats in 2006.   Xu et al., Env Sci Technol, 2008Xu, C., P. H. Santschi, J. Y. Zhong, P. G. Hatcher, A. J. Francis, C. J. Dodge, K. A. Roberts, C. C. Hung, and B. D. Honeyman. Colloidal Cutin-Like Substances Cross-Linked to Siderophore Decomposition Products Mobilizing Plutonium from Contaminated Soils.  Environmental Science & Technology  42:8211-8217 DOI:  10.1021/es801348t; Schwantes and Santschi, Radiochim Acta, 2010Schwantes, J.M., and P.H. Santschi. Mechanisms of Plutonium sorption to mineral oxide surfaces: New insights with implications to colloid-enhanced migration.  Radiochimica Acta  98(9-11):737-742 DOI:  10.1524/ract.2010.1775.
  • Developed and demonstrated non-invasive geophysical techniques to monitor microbial processes in the subsurface. Hubbard et al., Env Sci Technol, 2008.Hubbard, S. S., K. Williams, M. E. Conrad, B. Faybishenko, J. Peterson, J. S. Chen, P. Long, and T. Hazen. Geophysical monitoring of hydrological and biogeochemical transformations associated with Cr(VI) bioremediation.  Environmental Science & Technology 42(10):3757-3765 DOI:  10.1021/es071702s
  • Microbial-induced calcite precipitation demonstration project in the Snake River Plain Aquifer succeeds as an approach for removing divalent cations in aquifers. Fujita et al., Env Sci Technol. 2008.Fujita, Y., J. L. Taylor, T. L. T. Gresham, M. E. Delwiche, F. S. Colwell, T. L. McLing, L. M. Petzke, and R. W. Smith. Stimulation of microbial urea hydrolysis in groundwater to enhance calcite precipitation.  Environmental Science & Technology  42:3025-3032 DOI:  10.1021/es702643g

2007

  • Multiple studies demonstrate that the incorporation of hydro-biogeochemical process understanding into HPC-based reactive transport model codes enables predictive understanding of microbially-mediated biogeochemical reactions in natural, heterogeneous media.   Yabusaki et al, J Cont Hydrol, 2007Yabusaki, S. B., Y. Fang, P. E. Long, C. T. Resch, A. D. Peacock, J. Komlos, P. R. Jaffe, S. J. Morrison, R. D. Dayvault, D. C. White, and R. T. Anderson. Uranium removal from groundwater via in situ biostimulation: Field-scale modeling of transport and biological processes.  Journal of Contaminant Hydrology  93(1):216-235 DOI:  10.1016/j.jconhyd.2007.02.005; Li et al, Env Sci Technol, 2009Li, L., C. I. Steefel, K. H. Williams, M. J. Wilkins, and S. S. Hubbard. Mineral Transformation and Biomass Accumulation Associated With Uranium Bioremediation at Rifle, Colorado.  Environmental Science & Technology  43(14):5429-5435 DOI:  10.1021/es900016v; Li et al, J Cont Hydrol, 2010Li, L., C. I. Steefel, M. B. Kowalsky, A. Englert, and S. S. Hubbard. Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during biostimulation experiments at Rifle, Colorado.  Journal Of Contaminant Hydrology 112(1-4 Special Issue):45-63 DOI:  10.1016/j.jconhyd.2009.10.006; Li et al, Env Sci Technol, 2011 Li, L., N. Gawande, M. B. Kowalsky, C. I. Steefel, and S. S. Hubbard. Physicochemical heterogeneity controls on uranium bioreduction rates at the field scale.  Environmental Science & Technology  45 (23): 9959-9966 DOI:  10.1021/es201111y ; Yabusaki et al, J Cont Hydrol, 2011Yabusaki, S.B.; Fang, Y.; Williams, K.H.; Murray, C.J.; Ward, A.L.; Dayvault, R.D.; Waichler, S.R.; Newcomer, D.R.; Spane, F.A., Long, P.E. Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment.  Journal of Contaminant Hydrology  126(3-4): 271-290 DOI:  10.1016/j.jconhyd.2011.09.002; Druhan et al., Env Sci Technol, 2012Druhan, J. L., C. I. Steefel, S. Molins, K. H. Williams, M. E. Conrad, and D. J. DePaolo. Timing the Onset of Sulfate Reduction over Multiple Subsurface Acetate Amendments by Measurement and Modeling of Sulfur Isotope Fractionation.  Environmental Science & Technology  46:8895-8902 DOI:  10.1021/es302016p ; Zachara et al., J Cont Hydrol, 2013Zachara, J. M., P. E. Long, J. Bargar, J. A. Davis, P. Fox, J. K. Fredrickson, M. D. Freshley, A. Konopka, C. Liu, J. P. McKinley, M. Rockhold, K. H. Williams, and S. B. Yabusaki. Persistence of uranium groundwater plumes: Contrasting mechanisms at two DOE sites in the groundwater-river interaction zone.  Journal of Contaminant Hydrology  147:45-72 DOI:  10.1016/j.jconhyd.2013.02.001; Druhan et al, Geochim Cosmochim Acta, 2014Druhan, J.L.; Steefel, C.I.; Conrad, M.E.; DePaolo, D.J. A large column analog experiment of stable isotope variations during reactive transport: I. A comprehensive model of sulfur cycling and δ34S fractionation.  Geochimica et Cosmochimica Acta  124:366 - 393 DOI:  10.1016/j.gca.2013.08.037

    Druhan, J. L., M. Bill, H. Lim, C. Wu, M. E. Conrad, K. H. Williams, D. J. DePaolo, and E. L. Brodie. A large column analog experiment of stable isotope variations during reactive transport: II. Carbon mass balance, microbial community structure and predation.  Geochimica Et Cosmochimica Acta  124:394-409 DOI:  10.1016/j.gca.2013.08.036
    ; Bao et al., Env Sci Technol, 2014Bao, C., H. Wu, L. Li, D. Newcomer, P. E. Long, and K. H. Williams. Uranium Bioreduction Rates across Scales: Biogeochemical Hot Moments and Hot Spots during a Biostimulation Experiment at Rifle, Colorado.  Environmental Science & Technology  48(17):10116-10127 DOI:  10.1021/es501060d; Yabusaki et al, Env Sci Technol, 2017Yabusaki, Steven B., Michael J. Wilkins, Yilin Fang, Kenneth H. Williams, Bhavna Arora, John Bargar, Harry R. Beller, Nicholas J. Bouskill, Eoin L. Brodie, John N. Christensen, Mark E. Conrad, Robert E. Danczak, Eric King, Mohamad R. Soltanian, Nicolas F. Spycher, Carl I. Steefel, Tetsu K. Tokunaga , Roelof Versteeg, Scott R. Waichler, and Haruko M. Wainwright. Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.  Environmental Science & Technology  51(6):3307-3317 DOI:  10.1021/acs.est.6b04873.
  • First demonstration of the performance of a functional gene microarray called “GeoChip,” which had 24,243 oligonucleotide probes covering >10,000 genes in >150 functional groups, including ones that involved nitrogen, carbon, sulfur and phosphorus cycling. Performance characteristics were demonstrated on groundwater samples contaminated with uranium for the SBR-supported Y-12 (Oak Ridge) field site.   He et al., ISME J, 2007He, Z. L., T. J. Gentry, C. W. Schadt, L. Y. Wu, J. Liebich, S. C. Chong, Z. J. Huang, W. M. Wu, B. H. Gu, P. Jardine, C. Criddle, and J. Zhou. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME Journal 1:67-77 DOI: 10.1038/ismej.2007.2.
  • First publications from one of the SciDAC projects (established in 2006), which contributes to the continued development of continuum- and pore-scale reactive transport models.   Tartakovsky et al., Water Res Res, 2007Tartakovsky, A. M., P. Meakin, T. D. Scheibe, and B. D. Wood. A smoothed particle hydrodynamics model for reactive transport and mineral precipitation in porous and fractured porous media. Water Resources Research 43(5) DOI: 10.1029/2005WR004770; Tartakovsky et al., J Comp Physics, 2007Tartakovsky, A. M., P. Meakin, T. D. Scheibe, and R. M. E. West. Simulations of reactive transport and precipitation with smoothed particle hydrodynamics. Journal of Computational Physics 222:654-672 DOI: 10.1016/j.jcp.2006.08.013; Scheibe et al., J Physics Conf Series, 2007Scheibe, T.D., A.M. Tartakovsky, D.M. Tartakovsky, G.D. Redden, and P. Meakin. Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes. Journal of Physics: Conference Series 78(1):012063 DOI: 10.1088/1742-6596/78/1/012063.
  • BER managers establish three IFRC (Integrated Field Research Challenge) sites to demonstrate the value of integrating field-based experimentation with modeling/simulation (demonstrating “MODEX”). The sites were at the Oak Ridge Y-12 Site, the Rifle UMTRA Site in Colorado, and the Hanford Site.

2006

  • BER transitions the NABIR program into the Environmental Remediation Sciences Program (ERSP).
  • Demonstration of a pilot-scale, in situ process to immobilize uranium, nitrate and other contaminants at the Field Research Center in Oak Ridge, TN.   Wu, et al., Env Sci Technol, 2006Wu, W. M., J. Carley, M. Fienen, T. Mehlhorn, K. Lowe, J. Nyman, J. Luo, M. E. Gentile, R. Rajan, D. Wagner, R. F. Hickey, B. H. Gu, D. Watson, O. A. Cirpka, P. K. Kitanidis, P. M. Jardine, and C. S. Criddle. Pilot-scale in situ bioremediation of uranium in a highly contaminated aquifer. 1. Conditioning of a treatment zone. Environmental Science & Technology 40:3978-3985 DOI: 10.1021/es051954y; Wu et al., Env Sci Technol, 2006Wu, W. M., J. Carley, T. Gentry, M. A. Ginder-Vogel, M. Fienen, T. Mehlhorn, H. Yan, S. Caroll, M. N. Pace, J. Nyman, J. Luo, M. E. Gentile, M. W. Fields, R. F. Hickey, B. H. Gu, D. Watson, O. A. Cirpka, J. Z. Zhou, S. Fendorf, P. K. Kitanidis, P. M. Jardine, and C. S. Criddle. Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of U(VI) and geochemical control of U(VI) bioavailability. Environmental Science & Technology 40:3986-3995 DOI: 10.1021/es051960u.
  • First results from an in situ field experiment at the Field Research Center in Oak Ridge, TN on the effectiveness of an experiment to stimulate the growth of bacteria and to thereby limit the movement of uranium out of micropores into the surrounding groundwater. Scheibe et al., Geosphere, 2006Scheibe, T. D., Y. L. Fang, C. J. Murray, E. E. Roden, J. S. Chen, Y. J. Chien, S. C. Brooks, and S. S. Hubbard. Transport and biogeochemical reaction of metals in a physically and chemically heterogeneous aquifer. Geosphere 2:220-235 DOI: 10.1130/GES00029.1.
  • First demonstration of the performance of a (16S) DNA microarray called “PhyloChip,” which had 500,000 probes, to monitor changes in bacterial populations during an in-situ field experiment to reduce uranium in contaminated groundwater. Brodie et al., Appl Env Microbiol, 2006Brodie, E. L., T. Z. DeSantis, D. C. Joyner, S. M. Baek, J. T. Larsen, G. L. Andersen, T. C. Hazen, P. M. Richardson, D. J. Herman, T. K. Tokunaga, J. M. M. Wan, and M. K. Firestone. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Applied and Environmental Microbiology 72:6288-6298 DOI: 10.1128/AEM.00246-06. See this Berkeley Lab News article for more.
  • BER managers establish two SciDAC projects in 2006 in collaboration with the DOE Office if Advanced Scientific Computing Research (ASCR).
    • One project at LANL, led by Peter Lichtner, leads to the development of the parallelized PFLOTRAN HPC code. Hammond and Lichtner, Water Res Res, 2010Hammond, G. E., and P. C. Lichtner. Field-scale model for the natural attenuation of uranium at the Hanford 300 Area using high-performance computing. Water Resources Research 46(9):31 DOI: 10.1029/2009WR008819; Hammond et al., J Cont Hydrol, 2011Hammond, GE; Lichtner, PC; Rockhold, ML. Stochastic simulation of uranium migration at the Hanford 300 Area. Journal Of Contaminant Hydrology 120-21:115-128 DOI: 10.1016/j.jconhyd.2010.04.005.
    • The second project at PNNL, led by Tim Scheibe, is one of the first efforts to develop an integrated multi-scale modeling framework using hybrid numerical methods to link models from the continuum, to pore, to sub-pore scales.   Tartakovsky et al., SIAM J Sci Comput, 2008Tartakovsky, A. M., D. M. Tartakovsky, T. D. Scheibe, and P. Meakin. Hybrid Simulations of Reaction-Diffusion Systems in Porous Media. SIAM Journal on Scientific Computing 30:2799-2816 DOI: 10.1137/070691097; Palmer et al., Int J High Perf Comp App, 2010Palmer, B., V. Gurumoorthi, A. Tartakovsky, and T. Scheibe. A Component-Based Framework For Smoothed Particle Hydrodynamics Simulations Of Reactive Fluid Flow In Porous Media. The International Journal of High Performance Computing Applications 24(2):228-239 DOI: 10.1177/1094342009358415; Ryan, et al., J Cont Hydrol, 2011Ryan, E.M., A.M. Tartakovsky, and C. Amon. Pore-scale modeling of competitive adsorption in porous media. Journal Of Contaminant Hydrology 120-21:56-78 DOI: 10.1016/j.jconhyd.2010.06.008; Battiato et al., Adv Water Resour, 2011Battiato, I., D. M. Tartakovsky, A. M. Tartakovsky, and T.D. Scheibe. Hybrid models of reactive transport in porous and fractured media. Advances In Water Resources 34(9):1140-1150 DOI: 10.1016/j.advwatres.2011.01.012; Scheibe et al., Groundwater, 2015Scheibe, T. D., E. M. Murphy, X. Chen, A. K. Rice, K. C. Carroll, B. J. Palmer, A. M. Tartakovsky, I. Battiato, and B. D. Wood. An analysis platform for multiscale hydrogeologic modeling with emphasis on hybrid multiscale methods. Groundwater 53(1):38-56 DOI: 10.1111/gwat.12179.

2005

  • Discovered microbial “nanowires” and additional studies demonstrated the conductivity of microbial pili.   Reguera et al, Nature, 2005Reguera, G., K. D. McCarthy, T. Mehta, J. S. Nicoll, M. T. Tuominen, and D. R. Lovley. Extracellular electron transfer via microbial nanowires. Nature 435:1098-1101 DOI: 10.1038/nature03661; Summers et al., Science, 2010Summers, Z. M., H. Fogarty, C. Leang, A. E. Franks, N. S. Malvankar, and D. R. Lovley. 2010. Direct exchange of electrons within aggregates of an evolved syntrophic co-culture of anaerobic bacteria. Science 330:1413-1415. 10.1126/science.1196526
    NOT SBR Funded.
    ; Malvankar et al., Nature Nano, 2011Malvankar, N. S., M. Vargas, K. P. Nevin, A. E. Franks, C. Leang, B.-C. Kim, K. Inoue, T. Mester, S. F. Covalla, J. P. Johnson, V. M. Rotello, M. T. Tuominen, and D. R. Lovley. 2011. Tunable metallic-like conductivity in nanostructured biofilms comprised of microbial nanowires. Nature Nanotechnology 6:573-579. 10.1038/nnano.2011.119
    NOT SBR Funded.
    . Controversy remains over whether the microbial “nanowires” identified by other scientists are conductive. Gorby et al., PNAS, 2006Gorby, Y.A., S. Yanina, J.S. McLean, K.M. Rosso, D. Moyles, A. Dohnalkova, T.J. Beveridge, I.S. Chang, B.H. Kim, K.S. Kim, D.E. Culley, S.B. Reed, M.F. Romine, D.A. Saffarini, E.A. Hill, L. Shi, D.A. Elias, D.W. Kennedy, G. Pinchuk, K. Watanabe, S. Ishii, B. Logan, K.H. Nealson, and J.K. Fredrickson. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. PNAS 103(30): 11358-11363 DOI: 10.1073/pnas.0604517103 and his subsequent publications.
  • First field demonstration of the use of stable isotope probing to determine which microbes reduced uranium at the Rifle, CO UMTRA Site, and the impact of microbiological and geochemical heterogeneities on uranium reduction. Chang, et al., Env Sci Technol, 2005Chang, Y.-J., P.E. Long, R. Geyer, A.D. Peacock, C.T. Resch, K. Sublette, S. Pfiffner, A. Smithgall, R.T. Anderson, H.A. Vrionis, J.R. Stephen, R. Dayvault, I. Ortiz-Bernard, D.R. Lovley, and D.C. White. Microbial Incorporation of 13C-Labeled Acetate at the Field Scale: Detection of Microbes Responsible for Reduction of U(VI). Environmental Science & Technology 39(23):9030-9048 DOI: 10.1021/es051218u; Vrionis et al., Appl Env Micro, 2005Vrionis, H. A., R. T. Anderson, I. Ortiz-Bernad, K. R. O'Neill, C. T. Resch, A. D. Peacock, R. Dayvault, D. C. White, P. E. Long, and D. R. Lovley. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Applied and Environmental Microbiology 71:6308-6318 DOI: 10.1128/AEM.71.10.6308-6318.2005.

2004

  • First use of x-ray microscopy imaging techniques to characterize contaminant transformations by microbes. Kemner et al, Science, 2004Kemner, K.M., S.D. Kelly, B. Lai, J. Maser, E.J. O'Loughlin, D. Sholto-Douglas, Z. Cai, M.A. Schneegurt, C.F. Kulpa, Jr., and K.H. Nealson. Elemental and Redox Analysis of Single Bacterial Cells by X-ray Microbeam Analysis. Science 306:686-687 DOI: 10.1126/science.1103524.
  • First demonstration of a single-well “push-pull” test at the NABIR FRC to demonstrate the potential for bioreduction of uranium and technetium in groundwater. Istok et al., Env Sci Technol, 2004Istok, J.D., J.M. Senko, L.R. Krumholz, D. Watson, M.A. Bogle, A. Peacock, Y.-J. Chang, and D.C. White. In Situ Bioreduction of Technetium and Uranium in a Nitrate-Contaminated Aquifer. Environmental Science & Technology 38(2):468-475 DOI: 10.1021/es034639p; North et al., Appl Env Micro, 2004North, N.N., S.L. Dollhopf, L. Petrie, J.D. Istok, D.L. Balkwill, and J.E. Kostka. Change in Bacterial Community Structure during In Situ Biostimulation of Subsurface Sediment Co-contaminated with Uranium and Nitrate. Applied and Environmental Microbiology 70(8):4911-4920 DOI: 10.1128/AEM.70.8.4911-4920.2004.
  • Demonstrated that technetium transport in groundwater at the Hanford Site is retarded because of interactions between Tc and Fe, as well as microbial activity. Fredrickson et al, Geochem Cosmochim Acta, 2004Fredrickson, J.K., J.M. Zachara, D.W. Kennedy, R.K. Kukkadapu, J.P. McKinley, S.M. Heald, C. Liu, and A.E. Plymale. Reduction of TcO4- by sediment-associated biogenic Fe(II). Geochimica et Cosmochimica Acta 68(15):3171-3187 DOI: 10.1016/j.gca.2003.10.024; Zachara et al, Geochim Cosmochim Acta, 2007Zachara, J. M., S. M. Heald, B. H. Jeon, R. K. Kukkadapu, C. X. Liu, J. P. McKinley, A. C. Dohnalkova, and D. A. Moore. Reduction of pertechnetate [Tc(VII)] by aqueous Fe(II) and the nature of solid phase redox products. Geochimica et Cosmochimica Acta 71:2137-2157 DOI: 10.1016/j.gca.2006.10.025.

2003

  • First field-based studies to demonstrate microbially-based immobilization of uranium in groundwater at a contaminated DOE site - the Old Rifle, CO UMTRA Site. Anderson et al., Appl Env Micro, 2003Anderson, R.T., H.A. Vrionis, I. Ortiz-Bernad, C.T. Resch, P.E. Long, R. Dayvault, K. Karp, S. Marutzky, D.R. Metzler, A. Peacock, D.C. White, M. Lowe, and D.R. Lovley. Stimulated in situ removal of U(VI) from groundwater of a uranium-contaminated aquifer.. Applied and Environmental Microbiology 69:5884-5891 DOI: 10.1128/AEM.69.10.
  • Multiple studies that make use of x-ray synchrotron capabilities help explain geochemical controls (calcium carbonate and other complexes in aqueous system) on bacterially-mediated reduction of U(VI).   Brooks et al., Env Sci Technol, 2003Brooks, S.C., J.K. Fredrickson, S.L. Carroll, D.W. Kennedy, J.M. Zachara, A.E. Plymale, S.D. Kelly, K.M. Kemner, and S. Fendorf. Inhibition of bacterial U(VI) reduction by calcium. Environmental Science & Technology 37(9):1850-1858 DOI: 10.1021/es0210042; Kelly et al., Physica Scripta, 2005Kelly, S. D., K. M. Kemner, S. C. Brooks, J. K. Fredrickson, S. L. Carroll, D. W. Kennedy, J. M. Zachara, A. E. Plymale, and S. Fendorf. Ca-UO2-CO3 complexation- Implications for bioremediation of U(VI). Physica Scripta T115:915-917 DOI: 10.1238/Physica.Topical.115a00915; Dong and Brooks, Env Sci Technol, 2006Dong, W. M., and S. C. Brooks. Determination of the formation constants of ternary complexes of uranyl and carbonate with alkaline earth metals (Mg2+, Ca2+, Sr2+, and Ba2+) using anion exchange method. Environmental Science & Technology 40:4689-4695 DOI: 10.1021/es0606327; Kelly et al., Geochim Cosmochim Acta, 2007Kelly, S. D., K. M. Kemner, and S. C. Brooks. X-ray absorption spectroscopy identifies calcium-uranyl-carbonate complexes at environmental concentrations. Geochimica et Cosmochimica Acta 71(4):821-834 DOI: 10.1016/j.gca.2006.10.013; Dong and Brooks, Env Sci Technol, 2008Dong, W. M., and S. C. Brooks. Formation of aqueous MgUO2(CO3)32- complex and uranium anion exchange mechanism onto an exchange resin. Environmental Science & Technology 42:1979-1983 DOI: 10.1021/es0711563.
  • Multiple experimental and computational studies demonstrate that many types of microbes transfer electrons to mineral surfaces.   Rosso et al., Geochim Cosmochim Acta, 2003Rosso, K.M., J.M. Zachara, J.K. Fredrickson, Y.A. Gorby, and S.C. Smith. Nonlocal bacterial electron transfer to hematite surfaces.  Geochimica et Cosmochimica Acta  67(5):1081-1087 DOI:  10.1016/S0016-7037(02)00904-3; Kerisit et al., Geochim Cosmochim Acta, 2006Kerisit, S.N., and K.M. Rosso. Computer Simulation of Electron Transfer at Hematite Surfaces.  Geochimica et Cosmochimica Acta 70(8):1888-1903 DOI:  10.1016/j.gca.2005.12.021; Kerisit et al., JPC C, 2007Kerisit, S.N., K.M. Rosso, M. Dupuis, and M. Valiev. Molecular Computational Investigation of Electron Transfer Kinetics across Cytochrome-Iron Oxide Interfaces. Journal of Physical Chemistry C 111(30):11363-11375 DOI: 10.1021/jp072060y; Fredrickson and Zachara, Geobiology, 2008Fredrickson, J. K., and J. M. Zachara. Electron transfer at the microbe-mineral interface: a grand challenge in biogeochemistry.  Geobiology  6:245-253 DOI:  10.1111/j.1472-4669.2008.00146.x; Reardon et al., Geobiology, 2010Reardon, C. L., A. C. Dohnalkova, P. Nachimuthu, D. W. Kennedy, D. A. Saffarini, B. W. Arey, L. Shi, Z. Wang, D. Moore, J. S. McLean, D. Moyles, M. J. Marshall, J. M. Zachara, J. K. Fredrickson, and A. S. Beliaev. Role of outer-membrane cytochromes MtrC and OmcA in the biomineralization of ferrihydrite by  Shewanella oneidensis  MR-1.  Geobiology  8:56-68 DOI:  10.1111/j.1472-4669.2009.00226.x, EMSL News article; Renslow et al., Phys Chem Chem Phys, 2013Renslow, R., J. Babauta, A. Kuprat, J. Schenk, C. Ivory, J. Fredrickson, and H. Beyenal. Modeling biofilms with dual extracellular electron transfer mechanisms.  Physical Chemistry Chemical Physics  DOI:  10.1039/C3CP53759E; Liu et al, JACS, 2013Liu, J., C. I. Pearce, C. Liu, Z. Wang, L. Shi, E. Arenholz, and K. M. Rosso. Fe3-xTixO4 nanoparticles as tunable probes of microbial metal oxidation.  Journal of the American Chemical Society  DOI:  10.1021/ja4015343, EMSL News article; White et al., PNAS, 2013White, G. F., Z. Shi, L. Shi, Z. Wang, A. C. Dohnalkova, M. J. Marshall, J. K. Fredrickson, J. M. Zachara, J. N. Butt, D. J. Richardson, and T. A. Clarke. Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals.  Proceedings of the National Academy of Sciences  110(16):6346-6351 DOI:  10.1073/pnas.1220074110, EMSL News article; Ha et al., Nature Comm, 2017, EMSL News articleHa, P.T. Ha, S.R. Lindemann, L. Shi, A.C. Dohnalkova, J.K. Fredrickson, M.T. Madigan, and H. Beyenal. Syntrophic Anaerobic Photosynthesis via Direct Interspecies Electron Transfer.  Nature Communications  8:13924 DOI:  10.1038/ncomms13924.  
  • Developed and tested hydrogeophysical methods for characterization of subsurface flow and reactive transport properties using noninvasive geophysical observations. Hubbard and Rubin, J Contam Hydrol, 2000Hubbard, S. and Y. Rubin. Hydrogeological parameter estimation using geophysical data: a review of selected techniques. Journal of Contaminant Hydrology 45(1-2):3-34 DOI: 10.1016/S0169-7722(00)00117-0; Hubbard et al, Water Res Res, 2001Hubbard, S.S., J. Chen, J. Peterson, E.L. Maier, K.H. Williams, D.J. Swift, B. Mailloux, and Y. Rubin. Hydrogeological characterization of the south oyster bacterial transport site using geophysical data. Water Resources Research 37(10):2431-2456 DOI: 10.1029/2001WR000279; Scheibe and Chien, Ground Water, 2003Scheibe T., and Y.-J. Chien. An Evaluation of Conditioning Data for Solute Transport Prediction. Groundwater 41(2):128-141 DOI: 10.1111/j.1745-6584.2003.tb02577.x; Scheibe et al., Geosphere, 2006Scheibe, T. D., Y. L. Fang, C. J. Murray, E. E. Roden, J. S. Chen, Y. J. Chien, S. C. Brooks, and S. S. Hubbard. Transport and biogeochemical reaction of metals in a physically and chemically heterogeneous aquifer. Geosphere 2:220-235 DOI: 10.1130/GES00029.1.

2002

  • BER managers establish the first MOU with the DOE Office of Legacy Management (LM) to enable BER-funded scientists to undertake sampling campaigns as well as in situ field research campaigns at the Old Rifle, CO UMTRA Site as well as other Uranium Mill Tailing Remedial Action (UMTRA) sites.
  • Multiple studies identify and characterize nano-crystalline and monomeric uranium reduction products. Suzuki et al, Nature, 2002Suzuki, Y., S.D. Kelly, K.M. Kemner, and J.F. Banfield. Nanometer-size products of uranium bioreduction. Nature 419(6903):134 DOI: 10.1038/419134a; O’Louglin et al., Env Sci Technol, 2003O'Loughlin, E.J., S.D. Kelly, R.E. Cook, R. Csencsits, and K.M. Kemner. Reduction of uranium(VI) by mixed Fe(II)/Fe(III) hydroxide (green rust): Formation of UO2 nanoparticles. Environmental Science & Technology 37:721-727 DOI: 10.1021/es0208409; Burgos et al, Geochim Cosmochim Acta, 2008Burgos, W. D., J. T. McDonough, J. M. Senko, G. Zhang, A. C. Dohnalkova, S. D. Kelly, Y. Gorby, and K. M. Kemner. Characterization of uraninite nanoparticles produced by Shewanella oneidensis MR-1. Geochimica et Cosmochimica Acta 72(20):4901-4915 DOI: 10.1016/j.gca.2008.07.016; Kelly et al., Env Sci Technol, 2008Kelly, S. D., K. M. Kemner, J. Carley, C. Criddle, P. M. Jardine, T. L. Marsh, D. Phillips, D. Watson, and W. M. Wu. Speciation of uranium in sediments before and after in situ biostimulation. Environmental Science & Technology 42(5):1558-1564 DOI: 10.1021/es071764i; Fletcher et al., Env Sci Technol, 2010Fletcher, K. E., M. I. Boyanov, S. H. Thomas, Q. Z. Wu, K. M. Kemner, and F. E. Loeffler. U(VI) Reduction to Mononuclear U(IV) by Desulfitobacterium Species. Environmental Science & Technology 44(12):4705-4709 DOI: 10.1021/es903636c.

2001

  • Several studies demonstrate that physical and geochemical processes control bacterial transport in groundwater.   Hubbard et al., Water Res Res, 2001Hubbard, S.S., J. Chen, J. Peterson, E.L. Maier, K.H. Williams, D.J. Swift, B. Mailloux, and Y. Rubin. Hydrogeological characterization of the south oyster bacterial transport site using geophysical data. Water Resources Research 37(10):2431-2456 DOI: 10.1029/2001WR000279; Hubbard and Rubin, J Contam Hydrol, 2000Hubbard, S. and Y. Rubin. Hydrogeological parameter estimation using geophysical data: a review of selected techniques. Journal of Contaminant Hydrology 45(1-2):3-34 DOI: 10.1016/S0169-7722(00)00117-0; Chen et al., Water Res Res, 2004Chen, J., S. Hubbard, Y. Rubin, C. Murray, E. Roden, and E. Majer. Geochemical characterization using geophysical data and Markov Chain Monte Carlo methods: A case study at the South Oyster bacterial transport site in Virginia. Water Resources Research 40:W12412 DOI: 10.1029/2003WR002883; Scheibe et al., Geosphere, 2006Scheibe, T. D., Y. L. Fang, C. J. Murray, E. E. Roden, J. S. Chen, Y. J. Chien, S. C. Brooks, and S. S. Hubbard. Transport and biogeochemical reaction of metals in a physically and chemically heterogeneous aquifer. Geosphere 2:220-235 DOI: 10.1130/GES00029.1; review in Scheibe et al., Groundwater, 2011Scheibe, T. D., S. S. Hubbard, T. C. Onstott, and M. F. DeFlaun. Lessons Learned from Bacterial Transport Research at the South Oyster Site. Groundwater 49:745-763 DOI: 10.1111/j.1745-6584.2011.00831.x.
  • Multiple studies significantly advance the development of reactive transport codes that incorporate mechanistic hydrogeochemical processes and parallelization of these codes to run on HPC systems.   Yeh et al, Adv Env Res, 2001Yeh, G.T., W.D. Burgos, and J.M. Zachara. Modeling and measuring biogeochemical reactions: System consistency, data needs, and rate formulation. Advances in Environmental Research 5:219-237 DOI: 10.1016/S1093-0191(00)00057-5; Gwo et al, Comp Geosci, 2001Gwo, J.P., E.F. D'Azevedo, H. Frenzel, M. Mayes, G.-T. Yeh, P.M. Jardine, K.M. Salvage, and F.M. Hoffman. HBGC123D: a high-performance computer model of coupled hydrogeological and biogeochemical processes. Computers & Geosciences 27(10): 1231-1242 DOI: 10.1016/S0098-3004(01)00027-9; Liu et al., Env Sci Technol, 2002; 2010Liu, C., J.M. Zachara, J.K. Fredrickson, D.W. Kennedy, and A. Dohnalkova. Modeling the Inhibition of the Bacterial Reduction of U(VI) by β-MnO2(s)Environmental Science & Technology 36(7):1452-1459 DOI: 10.1021/es011159u; Bea et al, J Cont Hydrol, 2013Bea, S.A., H. Wainwright, N. Spycher, B. Faybishenko, S.S. Hubbard, and M.E. Denham. Identifying key controls on the behavior of an acidic-U(VI) plume in the Savannah River Site using reactive transport modeling. Journal of Contaminant Hydrology 151:34-54 DOI: 10.1016/j.jconhyd.2013.04.005; Chang et al., J Env Chem Eng, 2014Chang, H.-S., C. Xu, K. A. Schwehr, S. Zhang, D. I. Kaplan, J. C. Seaman, C. Yeager, and P. H. Santschi. Model of Radioiodine Speciation and Partitioning in Organic-rich and Organic-poor Soils from the Savannah River Site. Journal of Environmental Chemical Engineering 2:1321-1330 DOI: 10.1016/j.jece.2014.03.009; Steefel et al, Comput Geosci, 2015Steefel, C., S. Yabusaki, and K. U. Mayer. Reactive transport benchmarks for subsurface environmental simulation. Special issue, Computational Geosciences 19(3):439-443 DOI: 10.1007/s10596-015-9499-2.
  • Demonstrated that cesium transport is retarded in Hanford Site vadose zone sediments due to interactions with soil mineral surfaces. Fundamental understanding enables the DOE Office of Environmental Management to make long-term stewardship decisions concerning cesium-contaminated soils and groundwater at the Hanford Site. McKinley et al, Env Sci Technol. 2001McKinley, J.P., C.J. Zeissler, J.M. Zachara, R.J. Serne, R.M. Lindstrom, H.T. Schaef, and R.D. Orr. Distribution and Retention of 137Cs in Sediments at the Hanford Site, Washington. Environmental Science & Technology 35(17):3433-3441 DOI: 10.1021/es0018116; Zachara et al., Geochim Cosmochim Acta, 2002Zachara, J.M., S.C. Smith, C. Liu, J.P. McKinley, R.J. Serne, and P.L. Gassman. Sorption of Cs+ to micaceous subsurface sediments from the Hanford site, USA. Geochimica et Cosmochimica Acta 66(2):193-211 DOI: 10.1016/S0016-7037(01)00759-1; Liu et al, Env Sci Technol, 2003Liu, C., J.M. Zachara, O. Qafoku, and S.C. Smith. Effect of Temperature on Cs+ Sorption and Desorption in Subsurface Sediments at the Hanford Site, U.S.A.. Environmental Science & Technology 37(12):2640-2645 DOI: 10.1021/es026221h; Liu et al., Geochim Cosmochim Acta, 2003Liu, C., J.M. Zachara, S.C. Smith, J.P. McKinley, and C.C. Ainsworth. Desorption kinetics of radiocesium from subsurface sediments at Hanford Site, USA. Geochimica et Cosmochimica Acta 67(16):2893-2912 DOI: 10.1016/S0016-7037(03)00267-9; Steefel et al., J Contam Hydrol, 2003Steefel, C.I., S. Carroll, P. Zaho, and S. Roberts. Cesium migration in Hanford sediment: a multisite cation exchange model based on laboratory transport experiments. Journal of Contaminant Hydrology 67(1-4):219-246 DOI: 10.1016/S0169-7722(03)00033-0; Lictner, Vadose Zone J, 2004Lichtner, P.C., S. Yabusaki, K. Pruess, and C.I. Steefel. Role of Competitive Cation Exchange on Chromatographic Displacement of Cesium in the Vadose Zone beneath the Hanford S/SX Tank Farm. Vadose Zone Journal 3:203-219 DOI: 10.2136/vzj2004.2030; Ainsworth, Geochim Cosmochim Acta, 2005Ainsworth, C. C., J. M. Zachara, K. Wagnon, S. McKinley, C. Liu, S. C. Smith, H. T. Schaef, and P. L. Gassman. Impact of highly basic solutions on sorption of Cs+ to subsurface sediments from the Hanford site, USA. Geochimica et Cosmochimica Acta 69:4787-4800 DOI: 10.1016/j.gca.2005.06.007.

2000

  • Demonstrated that uranium sorption and transport through disparate subsurface materials from across the DOE complex is governed by interactions with iron minerals.   Barnett et al., Soil Sci Soc Am J, 2000Barnett, M.O., P.M. Jardine, S.C. Brooks, and H.M. Selim. Adsorption and transport of uranium(VI) in subsurface media. Soil Science Society of America Journal  64(3):908-917 DOI: 10.2136/sssaj2000.643908x; Barnett et al., Env Sci Technol, 2002Barnett, M.O., P.M. Jardine, and S.C. Brooks. Uranium(VI) adsorption to heterogeneous subsurface media: Application of a surface complexation model. Environmental Science & Technology 36(5):937-942 DOI: 10.1021/es010846i.
  • Demonstrated that uranium (VI) could be reduced by microorganisms in the presence of a mineral (goethite), thereby making it potentially less mobile in groundwater. Fredrickson et al., Geochim Cosmochim Acta, 2000Fredrickson, J.K., J.M. Zachara, D.W. Kennedy, M.C. Duff, Y.A. Gorby, S.W. Li, and K.K. Krupka. Reduction of U(VI) in goethite (α-FeOOH) suspensions by a dissimilatory metal-reducing bacterium. Geochimica et Cosmochimica Acta 64(18):3085-3098 DOI: 10.1016/S0016-7037(00)00397-5.
  • First use of x-ray microscopy imaging techniques to characterize microbial biofilms. Labrenz et al., Science, 2000Labrenz, M., G.K. Druschel, T. Thomsen-Ebert, B. Gilbert, S.A. Welch, K.M. Kemner, G.A. Logan, R.E. Summons, G. De Stasio, P.L. Bond, B. Lai, S.D. Kelly, and J.F. Banfield. Formation of Sphalerite (ZnS) Deposits in Natural Biofilms of Sulfate-Reducing Bacteria. Science 290:1744-1747 DOI: 10.1126/science.290.5497.1744.
  • BER managers enabled the “opening” of a major DOE Site with subsurface radionuclide and heavy metal contamination in the groundwater and in the fractured bedrock/sediments to field-based scientific investigation through the establishment of the NABIR Field Research Center (FRC) at the Oak Ridge Y-12 Site in April 2000. BER managers worked with DOE’s NEPA Office and General Council to issue a Finding of No Significant Impact (FONSI) in April 2000 that was based on an Environmental Assessment (EA 1196) for the NABIR FRC. David Watson was the principal investigator. Establishing this site was especially important for enabling university-based scientists to conduct field-based in situ research at a contaminated DOE site.   See this PDF for more.
  • First demonstration of the use of a genetically engineering microorganism (GEM) (P. fluorescens HK44) in a “controlled release” setting, a lysimeter setup located at ORNL, to monitor the biodegradation of several polyaromatic hydrocarbons (naphthalene, anthracene, and phenanthrene) through fluorescence. GEMs were emplaced in the lysimeters in 1996. Ripp et al., Env Sci Technol, 2000Ripp, S., D.E. Nivens, Y. Ahn, C. Werner, J. Jarrell, J.P. Easter, C.D. Cox, R.S. Burlage, and G.S. Sayler. Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation process monitoring and control. Environmental Science & Technology 34 (5), 846-853 DOI: 10.1021/es9908319; Sayler and Ripp, Curr Opinion in Biotech, 2000Sayler, G.S., and S. Ripp. Field applications of genetically engineered microorganisms for bioremediation processes. Current Opinion in Biotechnology 11 (3), 286-289 DOI: 10.1016/S0958-1669(00)00097-5.
    • In a follow-up study conducted more than 12 years later by members of the same team, they identified genes in the lysimeter soils that appeared to be derived from HK44. See this report for more.

1999

  • First application of synchrotron x-ray techniques to examine redox reactions at the mineral-water interface in real time.   Demonstrated the in situ production of Mn(III) minerals as a product of the reduction of Mn(IV) minerals by Co(II)EDTA.   Fendorf et al., Geochem Cosmochim Acta, 1999Fendorf, S.E., P.M. Jardine, R.R. Patterson, D.L. Taylor, and S.C. Brooks. Pyrolusite surface transformations measured in real-time during the reactive transport of Co(II)EDTA2-. Geochimica et Cosmochimica Acta 63(19-20):3049-3057 DOI: 10.1016/S0016-7037(99)00232-X; Fendorf et al. ACS Symp Series, 1998Fendorf, S.E., P.M. Jardine, D.L. Taylor, S.C. Brooks, and E.A. Rochette. Auto-inhibition of oxide mineral reductive capacity toward Co(II)EDTA. In : Mineral-Water Interfacial Reactions: Kinetics and Mechanisms, eds. D. L. Sparks and T.J. Grundl, ACS Symposium Series 715:358-371 DOI: 10.1021/bk-1998-0715.ch018.
  • BER managers establish mechanisms through PNNL’s connections with managers of the Uranium Mill Tailing Remedial Action (UMTRA) program to allow the scientific community to obtain subsurface core and groundwater samples contaminated with uranium and other heavy metals from a DOE UMTRA Site (Shiprock, NM - 1998 and Gunnison, CO - 1999).
  • First studies to examine transport of hexavalent chromium in soils. Jardine et al, Env Sci Technol, 1999Jardine, P.M., S.E. Fendorf, M.A. Mayes, I.L. Larsen, S.C. Brooks, and W.B. Bailey. Fate and Transport of Hexavalent Chromium in Undisturbed Heterogeneous Soil. Environmental Science & Technology 33:2939-2944 DOI: 10.1021/es981211v.

1998

  • Publication of an estimate of the number of prokaryotes on Earth and the total amount of their cellular carbon. In part, used results from BER-funded studies of the deep subsurface microbiology. This paper spurred many follow-on research projects to assess the numbers of cells in the subsurface. Some environments have been well-explored. Many (e.g., fractured rock in marine settings) remain enigmatically hard to sample and characterize. Whitman et al., PNAS, 1998Whitman, W.B., D.C. Coleman, and W.J. Wiebe. Prokaryotes: The unseen majority. PNAS 95(12):6578-6583.

1997

  • Multiple publications describe deep subsurface sediment pore-size constraints on microbial activity, survival, biomass volumes, community composition and biodiversity from several different drilling campaigns:
    • Taylorsville Triassic Basin:   Thermophilic metal-reducing bacteria produce nanoparticulate magnetite in 2770m deep sediments. Onstott, et al., Geomicrobiol J, 1998Onstott, T.C., T.J. Phelps, F.C. Colwell, D.B. Ringelberg, D.C. White, D.R. Boone, J.P. McKinley, T.O. Stevens, P.E. Long, D.L. Balkwill, W.R. Griffin, and T. Kieft. Observations pertaining to the origin and ecology of microorganisms recovered from the deep subsurface of Taylorsville Basin, Virginia. Geomicrobiology Journal 15(4):353-385 DOI: 10.1080/01490459809378088; Liu and Phelps et al., Science, 1997Liu, S.V., J. Zhou, C. Zhang, D.R. Cole, M. Gajdarziska-Josifovska, and T.J. Phelps. Thermophilic Fe(III)-reducing bacteria from the deep subsurface: The evolutionary implications. Science 277:1106-1108 DOI: 10.1126/science.277.5329.1106.
    • Cerro Negro, NM Fredrickson, et al. Geomicrobiol J, 1997Fredrickson, J.K., J.P. McKinley, B.N. Bjornstad, P.E. Long, D.B. Ringelberg, D.C. White, L.R. Krumholz, J.M. Suflita, F.S. Clwell, R.M. Lehman, T.J. Phelps, and T.C. Onstott. Pore-size constraints on the activity and survival of subsurface bacteria in a late cretaceous shale-sandstone sequence, northwestern New Mexico. Geomicrobiology Journal 14(3): 183-202 DOI: 10.1080/01490459709378043; Ringelberg, D. B., et al., FEMS Microbiol Rev, 1997Ringelberg, D.G., S. Sutton, and D.C. White. Biomass, bioactivity and biodiversity: microbial ecology of the deep subsurface: analysis of ester-linked phospholipid fatty acids. FEMS Microbiology Reviews 20(3-4) 374-377 DOI: 10.1111/j.1574-6976.1997.tb00322.x.
    • Hanford Site (Yakima barricade)   Chandler et al., FEMS Microbiol Ecol, 1997Chandler, D.P., S.-M. Li, C.M. Spadoni, G.R. Drake, D.L. Balkwill, J.K. Fredrickson, and F.J. Brockman. A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment. FEMS Microbiology Ecology 23(2):131-144 DOI: 10.1111/j.1574-6941.1997.tb00397.x.
  • First “how-to” paper describing detailed methods for using signature lipid biomarkers for analyzing microbial communities. White and Ringelberg, 1997White D. C., and D. B. Ringelberg. 1997. Signature lipid biomarker analysis. In R. S. Burlage, R. Atlas, D. Stahl, G. Geesey, and G. Sayler (ed.), Techniques in Microbial Ecology. Oxford University Press, New York, NY. 225-272.

1996

  • Popular press article entitled “Microbes Deep inside the Earth,” which describes BER-funded research activities over the past 10 years to understand indigenous microbial communities that have existed within deep geological sediments that have been isolated for millions of years, how they have survived, and where they might have come from. Fredrickson and Onstott, Scientific American, 1996. Fredrickson, J.K. and T.C. Onstott. Microbes Deep Inside the Earth. Scientific American October 1996 Download PDF.
  • Review of methods to determining biomass, community structure and metabolic activity for microbial ecological studies. White et al, 1996. White, D.C., H.C. Pinkart, and D.B. Ringelberg. Biomass Measurements: Biochemical Approaches. Manual of Environmental Microbiology. American Society for Microbiology Press, Washington, DC. C.H. Hurst, G. Knudsen, M. McInerney, L.D. Stetzenach, and M. Walter (ed.).
  • Summary paper describing use of perfluorocarbon (PFC) tracers during multiple subsurface drilling/coring projects from the late 1980’s to the early 1990’s to constrain sampling for indigenous microorganisms. McKinley and Colwell, J. Microbiol Meth, 1996McKinley, J.P., and F.S. Colwell. Application of perfluorocarbon tracers to microbial sampling in subsurface environments using mud-rotary and air-rotary drilling techniques. Journal of Microbiological Methods 26:1-9 DOI: 10.1016/0167-7012(96)00826-3.
  • BER transitions the Subsurface Science Program (SSP) into the Natural and Accelerated Bioremediation Research (NABIR) program.
  • DOE Office of Environmental Management (EM) initiates the Environmental Management Sciences Program (EMSP) and engages managers from the DOE Office of Science (SC), including BER, to co-advise on the selection of projects and to co-manage the execution of selected projects.

1995

  • Identified indigenous chemolithotrophic bacteria in deep aquifers in Columbia River basalt (at the Hanford Site) and posited that their source of energy was dissolved hydrogen. While this work initiated much research on what the sources of energy are for indigenous chemolithotrophic bacteria in the deep subsurface, and it greatly stimulated NASA’s astrobiology program, it remains controversial to this day. Stevens and McKinley, Science, 1995Stevens, T.O., and J.P. McKinley. Lithoautotrophic Microbial Ecosystems in Deep Basalt Aquifers. Science 270:450-454 DOI: 10.1126/science.270.5235.450 .
  • Demonstrated the use of signature lipid biomarker analysis in determining the in situ viable biomass, community structure, and nutritional/physiologic status of the deep subsurface microbiota. Amy and Halderman (ed.), 1997Amy, P.S., and D.L. Halderman (eds.). Microbiology of the Terrestrial Deep Subsurface. CRC Press ISBN 9780849383625; White and Ringelberg, 1997White, D.C., and D.B. Ringelberg. Signature lipid biomarker analysis. In R.S. Burlage, R. Atlas, D. Stahl, G. Geesey, and G. Sayler (ed.), Techniques in Microbial Ecology Oxford University Press, New York, NY. 225-272.
  • Initiation of in situ field research at the South Oyster field site located in the coastal plain of the eastern U.S. on Nature Conservancy lands, to investigate the transport of bacteria in iron oxide-dominated sediments that were geologically relatively homogeneous (i.e., sandy sediments). Research was done under an MOU between DOE and the Nature Conservancy. Fuller et al., Water Res Res, 2000Fuller, M.E., H. Dong, B.J. Mailloux, T.C. Onstott, and M.F. DeFlaun. Examining bacterial transport in intact cores from Oyster, Virginia: Effect of sedimentary facies type on bacterial breakthrough and retention. Water Resources Research 36(9):2417-2431 DOI: 10.1029/2000WR900075; Mailloux et al., Water Res Res, 2003Mailloux, B.J., M.E. Fuller, T.C. Onstott, J. Hall, H. Dong, M.F. DeFlaun, S.H. Streger, R.K. Rothmel, M. Green, D.J.P. Swift, and J. Radke. The role of physical, chemical, and microbial heterogeneity on the field-scale transport and attachment of bacteria. Water Resources Research 39(6):1142 DOI: 10.1029/2002WR001591.
  • First studies to examine how well a complexant (ethylenediaminetetraacetic acid - EDTA) that was bound to a heavy metal (cobalt), retarded the transport of that heavy metal in groundwater. Jardine and Taylor, Geoderma, 1995Jardine, P., and D.L. Taylor. Fate and transport of ethylenediaminetetraacetate chelated contaminants in subsurface environments. Geoderma 67(1-2):125-140 DOI: 10.1016/0016-7061(94)00059-J; Jardine and Taylor, Geochim Cosmochim Acta, 1995Jardine, P., and D.L. Taylor. Kinetics and mechanisms of Co(II) EDTA oxidation by pyrolusite. Geochimica et Cosmochimica Acta 59(20):4193-4203 DOI: 10.1016/0016-7037(95)00295-B; Brooks et al, Geochim Cosmochim Acta, 1996Brooks, S.C., D.L. Taylor, and P.M. Jardine. Reactive transport of EDTA-complexed cobalt in the presence of ferrihydrite. Geochimica et Cosmochimica Acta 60(11):1899-1908 DOI: 10.1016/0016-7037(96)00064-6; Fendorf et al., Geochim Cosmochim Acta, 1998Fendorf, S.E., P.M. Jardine, R.R. Patterson, D.L. Taylor, and S.C. Brooks. Pyrolusite surface transformations measured in real-time during the reactive transport of Co(II)EDTA2-Geochimica et Cosmochimica Acta 63(19-20):3049-3057 DOI: 10.1016/S0016-7037(99)00232-X; Szecsody et al., Water Res Res, 1998Szecsody, J.E., A. Chilakapati, J.M. Zachara, and A.L. Garvin. Influence of iron oxide inclusion shape on CoII/IIIEDTA reactive transport through spatially heterogeneous sediment. Water Resources Research 34(10):2501-2514 DOI: 10.1029/98WR02405; Zachara et al., Geochim Cosmochim Acta, 2000Zachara, J.M., S.C. Smith, and J.K. Fredrickson. The effect of biogenic Fe(II) on the stability and sorption of Co(II)EDTA2- to goethite and a subsurface sediment. Geochimica et Cosmochimica Acta 64(8): 1345-1362 DOI: 10.1016/S0016-7037(99)00427-5.

1994

  • BER-funded scientists develop and test multi-level, in-well sampling technology for contaminated subsurface environments. Mailloux et al., Groundwater, 2003Mailloux, B.J., M.E. Fuller, G.F. Rose, T.C. Onstott, M.F. DeFlaun, E. Alvarez, C. Hemingway, R.B. Hallet, T.J. Phelps, and T. Griffin. Modular injection system, multilevel sampler, and manifold for tracer tests. Groundwater 41(6):816-827.
  • First study to show the importance of understanding evolutionary processes of subsurface bacteria. Compared 16S rRNA gene sequences from dissimilatory sulfate reducing bacteria to multi-enzyme activities involved in PLFA (phospholipid fatty acid) patterns. Kohring, et al. FEMS Microbiol Lett, 1994Kohring, L.L., D.B. Ringelberg, R. Devereux, D.A. Stahl, M.W. Mittelman, and D.C. White. Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria. FEMS Microbiology Letters 119(3):303-308 DOI: 10.1111/j.1574-6968.1994.tb06905.x.
  • Cored to a depth of about 2100m at a potential New Production Reactor site near Parachute, CO into Paleocene and Cretaceous sandstones. Led by J. Fredrickson and R. Colwell. Led to papers describing temperature, space limitations and hydrology constraints for microbial growth and activity, and thermophilic iron reducing cells. Liu et al., Science, 1997Liu, S.V., J. Zhou, C. Zhang, D.R. Cole, M. Gajdarziska-Josifovska, and T.J. Phelps. Thermophilic Fe(III)-reducing bacteria from the deep subsurface: The evolutionary implications. Science 277:1106-1108 DOI: 10.1126/science.277.5329.1106; Colwell et al., FEMS Microbiol Rev, 1997Colwell, F.S., T.C. Onstott, M.E. Delwiche, D. Chandler, J.K. Fredrickson, Q.-J. Yao, J.P. McKinley, D.R. Boone, R. Griffiths, T.J. Phelps, D. Ringelberg, D.C. White, L. LaFreniere, D. Balkwill, R.M. Lehman, J. Konisky, and P.E. Long. Microorganisms from deep, high temperature sandstones: constraints on microbial colonization. FEMS Microbiology Reviews 20:425-435 DOI: 10.1016/S0168-6445(97)00024-7.
  • Cored two holes at Cerro Negro, NM, to a depth of 240 meters into Cretaceous Epoch shales and sandstones. Led by P. Long and T. Kieft. Led to papers describing temperature, space limitations and hydrologic constraints for microbial growth and activity. David Boone isolated Shewanella CN32, a mesophilic, ferric-iron-reducing microbe from this campaign. Fredrickson, et al. Geomicrobiol J, 1997Fredrickson, J.K., J.P. McKinley, B.N. Bjornstad, P.E. Long, D.B. Ringelberg, D.C. White, L.R. Krumholz, J.M. Suflita, F.S. Clwell, R.M. Lehman, T.J. Phelps, and T.C. Onstott. Pore-size constraints on the activity and survival of subsurface bacteria in a late cretaceous shale-sandstone sequence, northwestern New Mexico. Geomicrobiology Journal 14(3): 183-202 DOI: 10.1080/01490459709378043; Ringelberg et al., FEMS Microbiol Rev, 1997Ringelberg, D.G., S. Sutton, and D.C. White. Biomass, bioactivity and biodiversity: microbial ecology of the deep subsurface: analysis of ester-linked phospholipid fatty acids. FEMS Microbiology Reviews 20(3-4) 374-377 DOI: 10.1111/j.1574-6976.1997.tb00322.x.
  • Summary paper in AGU’s EOS describing multiple drilling/coring campaigns funded by the BER’s Subsurface Science Program to investigate indigenous microbial communities in the deep subsurface. Balkwill et al., EOS, 1994: 75:385-396Balkwill, D.R., and the DOE Subsurface Science Program's Taylorsville Basin Working Group. DOE seeks origin of deep subsurface bacteria. EOS 75:385-396 DOI: 10.1029/94EO01023.

1993

  • BER managers hosted workshops at multiple DOE sites (e.g., Sandia, Los Alamos, Rocky Flats) to transfer understanding of how to conduct aseptic drilling and sample handling.
  • Field studies demonstrate that natural organic matter (NOM) migrates in groundwater in a sandy aquifer, and that this leads to the production of colloidal iron oxide due to redox reactions. Coastal plain field site in South Carolina. McCarthy et al., Env Sci Technol, 1993McCarthy, J.F., T.M. Williams, L. Liang, P.M. Jardine, A.V. Palumbo, L.W. Cooper, L.W. Jolley, and D.L. Taylor. Mobility of Natural Organic Matter in a Sandy Aquifer. Environmental Science & Technology 27:667-676 DOI: 10.1021/es00041a010; Liang et al., Geochim Cosmochim Acta, 1993Liang, L., J.F. McCarthy, L.W. Jolley, J.A. McNabb, and T.L. Mehlhorn. Iron Dynamics: Transformation of Fe(II)/Fe(III) during Injection of Natural Organic Matter in a Sandy Aquifer. Geochimica et Cosmochimica Acta 57(9):1987-1999 DOI: 10.1016/0016-7037(93)90088-E; Gu et al., Env Sci Technol, 1994Gu, B., J. Schmitt, Z. Chen, L. Liang, and J.F. McCarthy,. Adsorption-desorption of Natural Organic Matter on Iron-oxide: Mechanisms and Models. Environmental Science & Technology 28(1):38-46 DOI: 10.1021/es00050a007.
  • Lab studies highlight the importance of coupled processes governing the movement of co-contaminants (radionuclides in the presence of chelating agents) through soils. Jardine et al, Soil Sci Soc Am J, 1993Jardine, P.M., G.K. Jacobs, and G.V. Wilson. Unsaturated transport processes in undisturbed heterogeneous porous media: I. Inorganic contaminants. Soil Science Society of America Journal 57, 945-953 DOI: 10.2136/sssaj1993.03615995005700040012x; Jardine et al., Soil Sci Soc Am J, 1993Jardine, P.M., G.K. Jacobs, and J.D. O'Dell. Unsaturated transport processes in undisturbed heterogeneous porous media: II. Co-contaminants. Soil Science Society of America Journal 57:954-962 DOI: 10.2136/sssaj1993.03615995005700040013x.
  • Demonstrated that the bacterium Geobacter metallireducens was capable of coupling the complete oxidation of organic compounds (e.g., fatty acids, alcohols and monoaromatic compounds) to the reduction of iron and other metals. This work contributed to a realization that perhaps some types of bacteria could be used to transform heavy metals and radionuclides, thereby reducing their mobility in groundwater. Lovley et al., Arch Microbiol, 1993Lovley, D.R., S.J. Giovannoni, D.C. White, J.E. Champine, E.J.P. Phillips, Y.A. Gorby, and S. Goodwin. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Archives of Microbiology 159:336-344 DOI: 10.1007/BF00290916.
  • First study to demonstrate that sulfate-reducing bacteria (SRBs) reduce Fe(III) directly, thus leading to the formation of siderite.   Coleman et al., Nature, 1993Coleman, M.L., D.B. Hedrick, D.R. Lovley, D.C. White, and K. Pye. Reduction of Fe(III) in sediments by sulphate-reducing bacteria. Nature 361:436-438 DOI: 10.1038/361436a0.

1992

  • Cored to 9000 feet deep (>2770 meters) at Thorn Hill, VA (Taylorsville Basin) in collaboration with Texaco. Results from microbial studies published in 1998. Liu et al., Science, 1997Liu, S.V., J. Zhou, C. Zhang, D.R. Cole, M. Gajdarziska-Josifovska, and T.J. Phelps. Thermophilic Fe(III)-reducing bacteria from the deep subsurface: The evolutionary implications. Science 277:1106-1108 DOI: 10.1126/science.277.5329.1106; Onstott et al, Geomicrobiol J, 1998Onstott, T.C., T.J. Phelps, F.C. Colwell, D.B. Ringelberg, D.C. White, D.R. Boone, J.P. McKinley, T.O. Stevens, P.E. Long, D.L. Balkwill, W.R. Griffin, and T. Kieft. Observations pertaining to the origin and ecology of microorganisms recovered from the deep subsurface of Taylorsville Basin, Virginia. Geomicrobiology Journal 15(4):353-385 DOI: 10.1080/01490459809378088.
  • Identification of a novel thermophilic bacterium from the very deep subsurface (Bacillus infernus). Obtained from the Thorn Hill drilling campaign. Boone et al., Int J Syst Bact, 1995Boone, D.R., Y. Liu, Z.J. Zhao, D.L. Balkwill, G.R. Drake, T.O. Stevens, and H.C. Aldrich. Bacillus infernus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. International Journal of Systematic Bacteriology 45(3):441-448 DOI: 10.1099/00207713-45-3-441.
  • Thorn Hill campaign also resulted in the development of an “indigenous” tracer idea using community characterization of cells in the drilling fluid. The International Ocean Discovery Program (IODP) has expanded this capability and uses it today. Lehman et al., J Microbiol Meth, 1995Lehman, R., F.S. Colwell, D. Ringelberg, and D.C. White. Combined microbial community-level analyses for quality assurance of terrestrial subsurface cores. Journal of Microbiological Methods 22(3):263-281 DOI: 10.1016/0167-7012(95)00012-A.
  • First publications from SSP-funded scientists to model hydraulic properties in soils. Wilson et al., Soil Sci Soc Am J, 1992Wilson, G.V., P.M. Jardine, and J.P. Gwo. Modeling the Hydraulic Properties of a Multiregion Soil. Soil Science Society of American Journal 56:173101737 DOI: 10.2136/sssaj1992.03615995005600060012x; Gwo et al, J Hydrol, 1995Gwo, J.P., P.M. Jardine, G.V. Wilson, and G.T. Yeh. A multiple-pore-region concept for modeling mass transfer in subsurface media. Journal of Hydrology 164:217-237 DOI: 10.1016/0022-1694(94)02555-P.
  • Scientific understanding of how to use PLFA, a method for identifying viable microbes and their composition, led to the formation of a new small business called Microbial Insights (Knoxville, TN).

1991

  • Demonstration of an approach to integrate phylogenetic relationships with signature lipid biomarkers for methylotrophs.   Guckert, et al., Microbiol 1991Guckert, J.B., D.B. Ringelberg, D.C. White, R.S. Hanson, and B.J. Bratina. Membrane fatty acids as phenotypic markers in the polyphasic taxonomy of methylotrophs within the Proteobacteria. Microbiology 137:2631-2641 DOI: 10.1099/00221287-137-11-2631.
  • Developed comprehensive QA/QC procedures and protocols used in workshops in 1993 and widely disseminated updated guidelines and reviews including:  Fredrickson, Phelps and Kieft in Volumes 1-3 of Manual for Environmental Microbiology; 1996, 2001, 2007.

1990

  • First use of microspheres for QA/QC as part of the coring to a depth of 183m and sampling at a potential New Production Reactor (NPR) site at INEEL (Snake River Plain basalt). Also developed tracer approaches using argon gas. Led by Rick Colwell. Colwell et al., J Microbiol Methods, 1992Colwell, F.S., G.J. Stormberg, T.J. Phelps, S.A. Birnbaum, J. McKinley, S.A. Rawson, C. Veverka, S. Goodwin, P.E. Long, B.F. Russell, T. Garland, D. Thompson, P. Skinner, and S. Grover. Innovative techniques for collection of saturated and unsaturated subsurface basalts and sediments for microbiological characterization. Journal of Microbiological Methods 15:279-292 DOI: 10.1016/0167-7012(92)90047-8; McKinley and Colwell, J. Microbiol. Meth, 1996McKinley, J.P., and F.S. Colwell. Application of perfluorocarbon tracers to microbial sampling in subsurface environments using mud-rotary and air-rotary drilling techniques. Journal of Microbiological Methods 26:1-9 DOI: 10.1016/0167-7012(96)00826-3.
  • BER-funded scientists developed a preliminary design for remediating a chromium plume at the 100 Area of the Hanford Site, and provided to the DOE Office of Environmental Management (EM). EM implemented the In Site Redox Manipulation field project at the 100 Area.
  • BER’s Subsurface Science Program co-sponsors the First International Symposium on Microbiology of the Deep Subsurface.   WSRS Information Services, Aiken, SC. Held in Orlando, FL. ISSM has continued and grown every three years somewhere in the world (Bath, 1993; Davos, 1996; Vale, 1999; Copenhagen, 2002; Jackson WY, 2005; Shizuoka, 2008; Garmisch-Partenkirchen, 2011; Monterey, CA, 2014; Rotorua, NZ, 2017).
  • Cored to 190 meters deep into Miocene Epoch lake sediments at the Yakima barricade borehole on the Hanford Site. Description of the microbial community from this campaign described in Fredrickson et al., Mol Ecol, 1995Fredrickson, J.K., J.P. McKinley, S.A. Nierzwicki-Bauer, D.C. White, D.B. Ringelberg, S.A. Rawson, S.-M. Li, F.J. Brockman, and B.N. Bjornstadt. Microbialcommunity structure and biogeochemistry of Miocene subsurface sediments: implications for long-term microbial survival. Molecular Ecology 4:619-626 DOI: 10.1111/j.1365-294X.1995.tb00262.x.

1989

  • First concept paper that calls attention to the role of colloids in facilitating the transport of radionuclides in groundwater. McCarthy and Zachara, Env Sci Technol, 1989McCarthy, J., and J. Zachara. Subsurface transport of contaminants. Environmental Science & Technology 23(5):496-502 DOI: 10.1021/es00063a001.
  • Establishment of methods to recover deep terrestrial subsurface sediments for studies of anaerobic microbes/microbial communities. Phelps, et al., J. Microbiol. Methods, 1989Phelps, T.J., C.B. Fliermans, T.R. Garland, S.M. Pfiffner, and D.C. White. Methods for recovery of deep terrestrial subsurface sediments for microbiological studies. Journal of Microbiological Methods 9:267-279 DOI: 10.1016/0167-7012(89)90069-9.
  • Initial studies on the mechanisms for the retention of dissolved organic carbon by soils.   Jardine et al, Soil Sci Soc Am J, 1989Jardine, P.M., J.F. McCarthy, and N.L. Weber. Mechanisms of Dissolved Organic-Carbon Adsorption on Soil. Soil Science Society of America Journal 53(5): 1378-1385 DOI: 10.2136/sssaj1989.03615995005300050013x.

1988

  • Initial application of signature biomarkers (later known as Phospholipid Fatty Acid Analysis - PLFA) to identify methanotroph bacteria in subsurface environments. Ringelberg et al., FEMS Microbiol Ecol, 1988Ringelberg, D.B., J.D. Davis, G.A. Smith, S.M. Pfiffner, P.D. Nichols, J.S. Nickels, J.M. Henson, J.T. Wilson, M. Yates, D.H. Kampbell, H.W. Read, T.T. Stocksdale, and D.C. White. Validation of signature polar lipid fatty acid biomarkers for alkaline-utilizing bacteria in soils and subsurface aquifer materials. FEMS Microbiology Ecology 62:39-50 DOI: 10.1111/j.1574-6968.1989.tb03656.x.
  • Cored to 365-470 meters deep near Savannah River at C10 borehole, and used tracers and tried out methods for recovering microorganisms from deep subsurface sediments. See: First International Symposium on Microbiology of the Deep Subsurface, 1990Fliermans, C.B. and T.C. Hazen. Proceedings of the First International Symposium on Microbiology of the Deep Subsurface. WSRS Information Services, Aiken, SC. See also: Phelps et al., J Microbial Methods, 1989Phelps, T.J., C.B. Fliermans, T.R. Garland, S.M. Pfiffner, and D.C. White. Methods for recovery of deep terrestrial subsurface sediments for microbiological studies. Journal of Microbiological Methods 9:267-279 DOI: 10.1016/0167-7012(89)90069-9. In addition, nine papers by SSP investigators on the presence and activities of microorganisms from WSRS-SSP coreholes were published in a special issue of Geomicrobiol J. 1989Ghiorse, W.C. and F.J. Wobber (eds.). Special Issue. Geomicrobiology Journal 7(1-2) DOI: 10.1080/01490458909377845.

1986

  • BER managers established the Subsurface Microbial Culture Collection (SMCC) at Florida State University.
  • Cored to a depth of 265m deep and sampled clays, sediments, microbial communities, and their metabolic activities from the lower Tertiary Period and upper Cretaceous Epoch at three P-wells at Savannah River Site. Among the microbes discovered were aerobic methanotrophs. Multiple papers from the many groups involved are presented in a special issue of Geomicrobiol J, Vol 7(1-2), 1989Ghiorse, W.C. and F.J. Wobber (eds.). Special Issue. Geomicrobiology Journal 7(1-2) DOI: 10.1080/01490458909377845. Also see: Hazen et al, Microbiol Ecol, 1991Hazen, T.C., L. Jiménez, G. López de Victoria, and C.B. Fliermans. Comparison of bacteria from deep subsurface sediment and adjacent groundwater. Microbial Ecology 22(1):293-304 DOI: 10.1007/BF02540231.

1985

  • First demonstrations of a quantitative approach to study microbial communities from a wide number of environments using lipid analysis. Guckert et al, FEMS Microbiol Ecol, 1985Guckert, J.B., C.P. Antworth, P.D. Nichols, and D.C. White. Phospholipid, ester-linked fatty acid profiles as reproducible assays for changes in prokaryotic community structure of estuarine sediments.  FEMS Microbiology Ecology 31(3): 147-158 DOI: 10.1111/j.1574-6968.1985.tb01143.x; Vestal and White, Bioscience, 1989Vestal, J.R., and D.C. White. Lipid Analysis in Microbial Ecology: Quantitative approaches to the study of microbial communities. BioScience 39(8):535-541 DOI: 10.2307/1310976.

1984

  • BER establishes the Subsurface Science Program (SSP).

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