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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).

2017

  • 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.]
  • First demonstration that Archaea have CRISPR-Cas9 systems. [Burstein et al., Nature, 2017.] 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.]
  • 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.]

2016

  • Demonstrated that metabolic handoffs among microbial community members is critical for cycling nutrients. [Anantharaman et al., Nature Comm, 2016.] 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.] See  BER highlight for more.
  • Significantly expanded the “Tree of Life.”  [Hug et al., Nature Micro, 2016.]
  • 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 Communications, 2016.] 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.]
  • 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.]
  • 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.] 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.]

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, 2014; Kaplan et al., Crit Rev Env Sci and Tech, 2014.]
  • 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.]  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.]
  • 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.
  • 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, 2014; Xu et al., Env Sci Technol, 2015; DiDonato et al., Env Sci Technol, 2017; Lin et al., Env Sci Technol 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, 2014; Kersting, Inorganic Chemistry, 2013.]

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, 2013; Salehikhoo and Li, Geochim Cosmochim Acta, 2015; Zachara et al., Env Sci Technol, 2016; Wang and Li, Env Sci Technol, 2016.]
  • 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, 2013; Lee et al., Geochim Cosmochim Acta, 2014; Hug et al., Env Micro, 2016; Bao et al., Env Sci Technol, 2016; Janot et al., Env Sci Technol, 2016; Jewell et al, ISME J, 2016; Tokunaga et al., Vadose Zone J, 2016; Arora et al., Biogeochemistry, 2016; Wainwright et al., Water Res Res, 2016; Yabusaki et al, Env Sci Technol, 2017; Jewell et al., Microbe, 2017.]
  • Modeling results prove to be the key for discovering the genetic basis (i.e., the genes) for mercury methylation. [Parks et al, Science, 2013.] 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.]
  • 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, 2011; Chourey et al., Proteomics, 2013.]
  • 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.] 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, 2012; Kostka et al., J Bacteriol, 2012; Prakash et al., Int J Syst Evol Microbiol, 2012; Venkatramanan 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.] .  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, 2011; Li et al., Env Sci Technol, 2012; Li, et al., Env Poll Tox, 2012; Li et al., App Env Micro, 2014; Grandois et al., Geomicrobiology, 2017.]

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, 2011; Watson et al., Env Sci Technol, 2013; Tang et al., Env Sci Technol, 2013; Tang et al., Env Sci Technol, 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, 2010; Kaplan et al., Env Sci Technol, 2011; Xu et al., Env Sci Technol, 2011; Otasaka et al., Sci Total Env 2011; Chang et al., J Env Chem Eng, 2013; Santschi et al., App Geochem, 2016; Xu et al., J Env Radioactiv, 2016.]
  • 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, 2010; Schwehr et al., Sci Total Env, 2014.]

2009

  • Discovered that uranium can exist in the pentavalent oxidation state - U(V) in nature. [Ilton et al., Env Sci Technol, 2009.]  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, 2009; Fang et al. Appl Env Micro, 2012; Tartakovsky et al., Adv Water Resour, 2013.]

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, 2008; Schwantes and Santschi, Radiochim Acta, 2010.]
  • Developed and demonstrated non-invasive geophysical techniques to monitor microbial processes in the subsurface. [Hubbard et al., Env Sci Technol, 2008.]
  • 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.]

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, 2007; Li et al, Env Sci Technol, 2009, J Cont Hydrol, 2010, and Env Sci Technol, 2011; Yabusaki et al, J Cont Hydrol, 2011; Druhan et al., Geochim Cosmochim Acta, 2012; Zachara et al., J Cont Hydrol, 2013; Druhan et al, Geochim Cosmochim Acta, 2014; Bao et al., Env Sci Technol, 2014; Yabusaki et al, Env Sci Technol, 2017.]
  • 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, 2007.]
  • 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, 2007; Tartakovsky et al., J Comp Physics, 2007; Scheibe et al., J Physics Conf Series, 2007.]
  • 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, 2006; Wu et al., Env Sci Technol, 2006.]
  • 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, 2006.]
  • 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, 2006.] 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, 2010; Hammond et al., J Cont Hydrol, 2011.]
    • 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, 2008; Palmer et al., Int J High Perf Comp App, 2010; Ryan, et al., J Cont Hydrol, 2011; Battiato et al., Adv Water Resour, 2011; Scheibe et al., Groundwater, 2015.]

2005

  • Discovered microbial “nanowires” and additional studies demonstrated the conductivity of microbial pili.  Reguera et al, Nature, 2005, Summers et al., Science, 2010; Malvankar et al., Nature Nano, 2011. Controversy remains over whether the microbial “nanowires” identified by other scientists are conductive. [Gorby et al., PNAS, 2006 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, 2005; Vrionis et al., Appl Env Micro, 2005.]

2004

  • First use of x-ray microscopy imaging techniques to characterize contaminant transformations by microbes. [Kemner et al, Science, 2004.]
  • 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, 2004; North et al., Appl Env Micro, 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, 2004; Zachara et al, Geochim Cosmochim Acta, 2007.]

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, 2003
  • 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, 2003; Kelly et al., Physica Scripta, 2005; Dong and Brooks, Env Sci Technol, 2006; Kelly et al., Geochim Cosmochim Acta, 2007; Dong and Brooks, Env Sci Technol, 2008.]
  • Multiple experimental and computational studies demonstrate that many types of microbes transfer electrons to mineral surfaces.  [Rosso et al., Geochim Cosmochim Acta, 2003; Kerisit et al., Geochim Cosmochim Acta, 2006; Kerisit et al., JPC C, 2007; Fredrickson and Zachara, Geobiology, 2008; Reardon et al., Geobiology, 2010, EMSL News article; Renslow et al., Phys Chem Chem Phys, 2013; Liu et al, JACS, 2013, EMSL News article; White et al., PNAS, 2013, EMSL News article; Ha et al., Nature Comm, 2017, EMSL News article.] 
  • Developed and tested hydrogeophysical methods for characterization of subsurface flow and reactive transport properties using noninvasive geophysical observations. [Hubbard and Rubin, J Contam Hydrol, 2000; Hubbard et al, Water Res Res, 2001; Scheibe and Chien, Ground Water, 2003; Scheibe et al., Geosphere, 2006.]

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, 2002; O’Louglin et al., Env Sci Technol, 2003; Burgos et al, Geochim Cosmochim Acta, 2008; Kelly et al., Env Sci Technol, 2008; Fletcher et al., Env Sci Technol, 2010.]

2001

  • Several studies demonstrate that physical and geochemical processes control bacterial transport in groundwater.  [Hubbard et al., Water Res Res, 2001; Hubbard and Rubin, J Contam Hydrol, 2000; Chen et al., Water Res Res, 2004; Scheibe et al., Geosphere, 2006; review in Scheibe et al., Ground Water, 2011.]
  • 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, 2001; Gwo et al, Comp and Geosci, 2001; Liu et al., Env Sci Technol, 2002; 2010; Bea et al, J Cont Hydrol, 2013; Chang et al., J Env Chem Eng, 2014; Steefel et al, Comput Geosci, 2015.]
  • 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. 2001; Zachara et al., Geochim Cosmochim Acta, 2002; Liu et al, Env Sci Technol, 2003; Liu et al., Geochim Cosmochim Acta, 2003; Steefel et al., J Contam Hydrol. 2003; Lictner, Vadose Zone J, 2004; Ainsworth, Geochim Cosmochim Acta, 2005.]

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, 2000; Barnett et al., Env Sci Technol, 2002.]
  • 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, 2000.]
  • First use of x-ray microscopy imaging techniques to characterize microbial biofilms. [Labrenz et al., Science, 2000.]
  • 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, 2000; Sayler and Ripp, Curr Opinion in Biotech, 2000.]
    • 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., Geochim Cosmochim Acta, 1999.]
  • 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, 1999.]

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, 1998.]

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., Geomicrobiology J, 1998; Liu and Phelps et al., Science, 1997.]
    • Cerro Negro, NM [Fredrickson, et al. Geomicrobiology J, 1997; Ringelberg, D. B., et al., FEMS Microbiol. Rev., 1997.]
    • Hanford Site (Yakima barricade)  [Chandler et al., FEMS Microbiol Ecol, 1997.]
  • First “how-to” paper describing detailed methods for using signature lipid biomarkers for analyzing microbial communities. [White 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. Download PDF.]
  • Review of methods to determining biomass, community structure and metabolic activity for microbial ecological studies. [White , D. C., H. C. Pinkart, and D. B. Ringelberg. 1996. In C. H. Hurst, G. Knudsen, M. McInerney, L. D. Stetzenach, and M. Walter (ed.), Manual of Environmental Microbiology. American Society for Microbiology Press, Washington, DC. 91-10.]
  • 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, 1996.
  • 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, 1995.]
  • 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. In DL Haldeman (ed.), The Microbiology of the Terrestrial Deep Subsurface. 1995? CRC Press, Lewis Publishers, Boca Raton, FL. 119-136. Also, White and Ringelberg, 1995?
  • 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. [DeFlaun and Onstott et al., Water Res Res, 2000; DeFlaun and Onstott et al., Water Res Res, 2000.]
  • 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, 1995; Jardine and Taylor, Geochim Cosmochim Acta, 1995; Brooks et al, Geochim Cosmochim Acta, 1996; Fendorf et al., Geochim Cosmochim Acta, 1998; Szecsody et al., Water Res Res, 1998; Zachara et al., Geochim Cosmochim Acta, 2000.]

1994

  • BER-funded scientists develop and test multi-level, in-well sampling technology for contaminated subsurface environments. [Mailloux et al., Ground Water, 2003.]
  • 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, 1994.]
  • 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, 1997; Colwell et al., FEMS Microbiology Reviews, 1997.]
  • 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. Geomicrobiology J, 1997; Ringelberg, D. B., et al., FEMS Microbiology Reviews, 1997.]
  • 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: 75:385-396.]

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, 1993; Liang et al., Geochim Cosmochim Acta, 1993; Gu et al., Env Sci Technol, 1994.]
  • 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, 1993; Jardine et al., Soil Sci Soc Am J, 1993.]
  • 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, 1993.]
  • First study to demonstrate that sulfate-reducing bacteria (SRBs) reduce Fe(III) directly, thus leading to the formation of siderite.  [Coleman et al., Nature, 1993.]

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, 1997; Onstott et al, Geomicrobiol J, 1998.]
  • 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, 1995.]
  • 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, 1995.]
  • First publications from SSP-funded scientists to model hydraulic properties in soils. [Wilson et al., Soil Sci Soc Am J, 1992; Gwo et al, J Hydrol, 1995.]
  • 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., J Gen Microbiol 1991.]
  • 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, 1992.]
  • 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, 1995:  4(5): 619-626.

1989

  • First concept paper that calls attention to the role of colloids in facilitating the transport of radionuclides in groundwater. [McCathy and Zachara, Env Sci Technol, 1989.]
  • Establishment of methods to recover deep terrestrial subsurface sediments for studies of anaerobic microbes/microbial communities. [Phelps, et al., J. Microbiol. Methods, 1989.]
  • Initial studies on the mechanisms for the retention of dissolved organic carbon by soils.  [Jardine et al, Soil Sci Soc Am J, 1989.]

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, 1988.]
  • 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.  1990.  WSRS Information Services, Aiken, SC. See also: Phelps and Fliermans et al., J Microbial Methods. 9: 276-279, 1989. 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 Geomicrobiology J. See: 1999 Vol 7(12) edited by W.C. Ghiorse and F. J. Wobber.

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 Geomicrobiology J, Vol 7(1-2), 1989. Also see: Hazen et al, Microbiol Ecol, 1991:  22:293-304.

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 Lett, 1985; Vestal and White, Bioscience, 1989.]

1984

  • BER establishes the Subsurface Science Program (SSP).

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