Biological and Environmental Sciences Directorate
2005 Research Highlights
Proteomics paper published in Science
A paper describing a study of gene expression in a
natural microbial biofilm community was published
recently in Science. The researchers used mass
spectrometry-based proteomics methods to determine the
functional activity of microbes in natural acid mining
drainage. Nathan VerBerkmoes, Manesh Shah, and Robert
Hettich of ORNL are among the co-authors.
Microbial communities play key roles in the Earth's biogeochemical cycles. Knowledge of the structure and activities in these communities is limited because analyses of microbial physiology and genetics have been largely confined to studies of organisms from the few lineages for which cultivation conditions have been determined. An additional limitation of purely culture-based studies is that potentially critical community and environmental interactions are not sampled. Recent acquisition of genomic data directly from natural samples has begun to reveal the gene content of communities and environments.
Using genomic and mass spectrometry-based proteomic methods, the authors evaluated gene expression, identified key activities, and examined partitioning of function in a natural acid mine drainage microbial biofilm community. They detected 2,036 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the most abundant biofilm organism, Leptosprillum group II. Proteins involved in protein refolding and response to oxidative stress appear to be highly expressed, suggesting that damage to biomolecules is a key challenge for survival. The authors validated and estimated the relative abundance and cellular localization of 216 conserved and 407 unique hypothetical proteins and showed that one abundant novel protein is a cytochrome central to iron oxidation and formation of acid mining drainage. In total, this approach enabled validation of predicted genes and estimation of the relative abundance and cellular localization of expressed proteins, provided clues to protein function, and yielded information about the physiological challenges faced by a self-sustaining, chemolithoautotrophic microbial community (i.e., a microbial community sustained by chemistry other than photosynthesis) in the environment.
R. J. Ram, N. C. VerBerkmoes, M. P. Thelen, G. W. Tyson, B. J. Baker, R. C. Blake II, M. Shah, R. L. Hettich, and J. F. Banfield. "Community proteomics of a natural microbial biofilm," Science 308 (5730): 1915-20 (24 June 2005).
Report published on the future of biomass as an industrial feedstock
The U.S. Department of Energy and the U.S. Department of
Agriculture are both strongly committed to expanding the
use of biomass as an industrial feedstock. In particular,
they support the use of biomass in the production of
fuels, chemicals, and other products as a way to reduce
the need for oil and gas imports; to support the growth
of agriculture, forestry, and rural economies; and to
foster major new domestic "biorefineries" to make a
variety of fuels and other products. As part of this
effort, the Biomass R&D Technical Advisory Committee,
a panel established by Congress to guide the future
direction of federally funded biomass R&D, envisioned
a 30% replacement of current U.S. petroleum consumption
with biofuels by 2030.
The report, Biomass as Feedstock for a Bioenergy and Bioproducts Industry, documents a study that was undertaken to determine whether the land resources of the United States are capable of producing a sustainable supply of biomass sufficient to meet the goal set by the advisory committee. Researchers found potential biomass resources exceeding 1.3 billion dry tons annually, enough to exceed the goal. The full potential of the resource could be realized around the mid-twenty-first century, when large-scale bioenergy and biorefinery industries are likely to exist. This projection is based on a more than sevenfold increase in production from the amount of biomass currently consumed for energy and biomass-based products.
The report has gained prominence in the current climate of rising fuel costs. President George W. Bush has highlighted it in recent speeches on the nation's energy needs, and Secretary of Energy Samuel W. Bodman has discussed the impact of the study on occasion, including his recent visit to ORNL. Others in the biomass field have included the results of the study in their analyses of the status of the bioenergy market and industry, so it is clear that the study is a critical, positive contribution to the field.
R. Perlack, L. Wright, A. Turhollow, R. Graham, B. Stokes, and D. Erbach. Biomass as Feedstock for a Bioenergy and Bioproducts Industry: The Technical Feasibility of a Billion-Ton Annual Supply, ORNL/TM-2005/66, DOE/GO-102995-2135 (2005).
Clustered climate regimes to analyze general circulation models
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Ensemble average of five "business-as-usual" global climate regime evolution curves. The number and its respective color identify each curve as being one of the 32 common climate regimes defined by applying Multivariate Spatio-Temporal Clustering. |
Changes in climate in response to greenhouse gas buildup impact the health of terrestrial ecosystems and the hydrologic cycle. The environmental conditions that influence plant and animal life are often mapped as ecoregions-land areas with similar combinations of environmental characteristics. ORNL scientists have used a modeling technique called multivariate spatio-temporal clustering (MSTC) to establish ecoregions that evolve over time. (Multivariate clustering classifies objects into groups based on the similarity of their properties.)
MSTC was applied to the monthly time series output from five 99-year "business-as-usual" transient simulations of the Parallel Climate Model (PCM) from 2000 to 2098.
MSTC establishes an exhaustive set of recurring climate regimes that form a "skeleton" based on the model output from throughout the occupied portion of a climate phase space formed by the characteristics being considered. The analysis included temperature, precipitation, and soil moisture.
Strong predicted year-to-year trends were revealed, including an increase in global desertification; a decrease in the cold, dry high-latitude conditions typical of North American and Asian winters; and significant warming in Antarctica and western Greenland.
MSTC is a powerful tool for helping model developers and environmental decision-makers understand long, complex time series predictions of models. It facilitates direct comparison of ensemble members, ensemble and temporal averages, and observational data because the derived climate regimes provide a basis for comparison.
F. M. Hoffman, W. W. Hargrove, D. J. Erickson, and R. J. Oglesby. "Using clustered climate regimes to analyze and compare predictions from fully coupled general circulation models," Earth Interactions 9(10): 1-27 (August 2005). Graphics and animations at http://climate.ornl.gov/pcm/.
The Collaborative Cross: A new approach to human health research
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The Collaborative Cross strategy will produce recombinant inbred mice specifically for the study of the relationship between complex genetic traits and disease. |
The most common and pervasive human health problems are caused by diseases with complex etiologies. Humans differ greatly in their genetic vulnerability to these common diseases, and the mechanisms that underlie susceptibility and progression are influenced by numerous genetic, developmental, and environmental factors.
ORNL's Collaborative Cross project will provide the international research community with a powerful resource for discovering and analyzing the contributions of those factors to the etiology of common, complex diseases. Eight carefully selected, genetically diverse mouse strains from around the world are being interbred at ORNL's Laboratory for Comparative Functional Genomics to produce a large population of recombinant inbred (RI) mouse strains designed specifically for complex trait analysis. Researchers expect about 1000 strains to be viable as interbreeding proceeds.
The large set of RI strains can support studies incorporating multiple variables into comprehensive statistical models of disease susceptibility, pathophysiology, and progression. The Collaborative Cross mouse population will be unique in providing a comprehensive body of genetic and physiological data derived from a common, reproducible, stable population, in contrast to previous mouse research based on isolated, transient crosses.
The effort will improve modeling of human populations and diseases because scientists will have 1000 lines of mice that carry the kinds of genetic diversity representative of people. Research with this large collection of isogenic strains under controlled environmental conditions will provide data that may ultimately be useful in diagnosing and treating an assortment of chronic human conditions, such as cancer, pulmonary and cardiovascular diseases, diabetes, and behavioral disorders. Software tools developed to predict phenotypes of RI mice will become the prototypes for applications to human health.
Several universities and institutions, including The Jackson Laboratory, the University of Tennessee, and the University of North Carolina, are participating in the effort.
The Complex Trait Consortium. "The Collaborative Cross, a community resource for the genetic analysis of complex traits," Nature Genetics 36(11):1-5 (November 2004).
ORNL DAAC for Biogeochemical Dynamics
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Scientists throughout the world are increasingly using DAAC data to study and assess the impacts of global change. |
Scientists throughout the world are using data from NASA's Distributed Active Archive Center (DAAC) at ORNL to study and assess the impacts of global change. The DAAC archives and distributes terrestrial biogeochemical dynamics data collected as part of the NASA's Earth Observing System (EOS) Program. The DAAC offers more than 760 data sets for four core activities: (1) field campaigns, (2) validation of remote sensing products, (3) regional and global studies, and (4) terrestrial ecosystem models.
Field campaigns combine ground-, aircraft-, and satellite-based measurements of biogeochemical features in specific ecosystems over a few years. They focus on a particular issue or set of issues and are crucial to providing an integrated understanding of biogeochemical dynamics that can be extended across spatial and temporal scales. Understanding environmental processes at multiple scales requires combining and comparing field-based measurements with remote sensing products.
The ORNL DAAC supports the validation of remotely sensed measurements by providing data, such as net primary productivity (NPP) and leaf area index (LAI), from global test sites for comparison with remote sensing products. The DAAC also offers subsets of selected Moderate-Resolution Imaging Spectroradiometer (MODIS) Land Products for the community to use in conjunction with flux measurements and other field data at the DAAC for studying local-, regional-, and global-scale processes. These subsets show pixel values of MODIS land products in ASCII format for a 7 × 7 km area centered on flux towers or field sites from around the world.
Models that simulate ecosystem properties and processes for improving our understanding of the structure and function of these ecosystems depend on data from multiple spatial and temporal scales. Biogeochemical dynamics data, such as those available from the ORNL DAAC, can be used to parameterize and validate terrestrial ecosystem models at local, regional, and global scales.
Archived models provide the methodological detail of numerical modeling studies to recreate published modeling results, enabling the synthesis of results across modeling studies and the investigation of new hypotheses. In addition, archived models allow determination of uncertainties for comparison with results from other models in assessment/policy studies. Model source code also allows others to see how models treat individual processes.
Data at the ORNL DAAC are available to the global change research community, policy makers, educators, and the general public at no charge. More than 770 data sets are available from the DAAC; in 2005, more than 560,000 data files were provided to more than 11,000 users.
Economically important plant pathogens compared
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Chromosome of Pss B728a with the outermost circle depicting open reading frames (ORFs) on the positive strand and the second circle depicting ORFs on the negative strand. The ORFs are color-coded based on the major grouping of role categories. |
A scientific study has compared the complete genomic sequences of two strains of Pseudomonas syringae. This economically important species of plant pathogenic bacteria consists of about 50 strains, which differ from each other in pathogenicity and host range. The study of the genomic differences between the two examples has resulted in a better understanding of the mechanisms leading to their pathogenicity. ORNL's Miriam Land and Frank Larimer were among the authors of the paper in which the study is described.
The two strains used in the study were Pseudomonas syringae pv. syringae B728a (Pss B728a) and P. syringae pv. tomato DC3000 (Pst DC3000). Pss B728a maintains a large population on the surface of healthy plants, where it is exposed to stressful conditions, such as dryness and sunlight, that are normally hostile to bacterial growth. When a plant's defenses are weakened, Pss can then invade host plants and initiate disease. Pst DC3000, however, colonizes poorly on the exterior of plants and multiplies mostly within them.
Because environmental conditions are more diverse for a plant's outer surface than they are for its interior, it had been hypothesized that Pss B728a has more genes that confer tolerance to environmental stress than Pst DC3000 has. The paper shows that among the nearly 1000 genes unique to Pss B728a are genes for resistance to ultraviolet light, copper, and streptomycin; tolerance to reactive oxygen species; promotion of ice crystal formation; and production of unique virulence proteins and the mechanisms to introduce them into the plant (type III secretion system effectors). This work serves as the beginning point for associating these genes with specific traits of the bacterial pathogens.
H. Feil, W. S. Feil, P. Chain, F. Larimer, G. DiBartolo, A. Copeland, A. Lykidis, S. Trong, M. Nolan, E. Goltsman, J. Thiel, S. Malfatti, J. E. Loper, A. Lapidus, J. C. Detter, M. Land, P. M. Richardson, N. C. Kyrpides, N. Ivanova, and S. E. Lindow. "Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000," Proceedings of the National Academy of Sciences of the United States of America 102 (31): 11064-69 (2005).
Genetic analysis could enhance soil carbon sequestration potential
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Conceptual diagram showing how genes for biomass distribution and tissue chemistry can influence carbon sequestration in soils. |
Scientists reached this conclusion by assembling an extensive above- and below-ground carbon inventory for more than 1000 hybrid poplar (Populus) trees. Field data collected over 3 years were combined with a newly developed genetic map to identify regions of the genome responsible for the distribution of dry mass to stems, branches, leaves, and roots. Results indicate that traits associated with distribution of dry mass were controlled by a small number of genes and that different genes controlled the above- and below-ground production of biomass. Such findings provide a glimpse into how fundamental knowledge gained through the basic biological sciences can address questions related to carbon management in terrestrial ecosystems.
S. D. Wullschleger, T. M. Yin, S. P. DiFazio, T. J. Tschaplinski, L. E. Gunter, M. F. Davis, and G. A. Tuskan. "Phenotypic variation in growth and biomass distribution for two advanced-generation pedigrees of hybrid poplar," Canadian Journal of Forest Research 35(8): 1779-89 (2005).
CSMB highlights: a new lab and two notable publications
The Center for Structural Molecular Biology (CSMB) is
leading research and development in neutron structure
analysis of proteins and protein complexes that will
support the user access and biology research programs at
the High Flux Isotope Reactor (HFIR) and the Spallation
Neutron Source (SNS) at ORNL. The CSMB has established
capabilities and critical expertise in areas extending
from the design, development, and operation of advanced
neutron instrumentation for biology to development of
isotopic labeling systems for biological macromolecules.
Advanced methods are being developed for the
characterization and analysis of the structure and
function of complex biological macromolecules that extend
from the atomic level of detail to their integrated
function in the molecular mechanisms of the cell.
Neutron scattering provides a unique, nondestructive probe of delicate biological materials and higher-order assemblies, and the design and production of hydrogen/deuterium (H/D)-labeled material permit selected parts of macromolecular structures to be highlighted and analyzed in situ. CSMB and the Life Sciences Division have established a Bio-Deuteration Laboratory for in vivo production of H/D-labeled bio-macromolecules to support the user research programs at HFIR and SNS.
In an article featured on the cover of Protein Science, William Heller and colleagues described a solution-scattering analysis of nonactivated and Ca2+-activated phosphorylase kinase that produced conformer models consistent with Ca2+-induced conformational changes in both the lobes and the interlobal bridges of the 1.3-MDa (αβγδ)4 hexadecameric complex. The modeling techniques developed and used in this work will enable functional models of multi-meric complexes to be derived from neutron scattering experiments at HFIR and at SNS.
In an article published in the Proceedings of the National Academy of Sciences and listed as a Research Highlight in Nature, Dean Myles and colleagues described the first example of a protein structure determined at cryogenic temperature (15 K) by neutron crystallography. Their work on the plant lectin Concanavalin A showed how the reduced dynamic disorder in the neutron structure at low temperature enabled twice as many bound water molecules to be identified at 15 K as at 293 K. This methodology opens up new categories of neutron protein crystallography, including freeze-trapped reaction and intermediate structures, that will be of interest to the development of the Macromolecular Diffractometer at SNS.
T. S. Priddy, B. A. Macdonald, W. T. Heller, O. W. Nadeau, J. Trewhella, and G. M. Carlson. "Ca2+-induced structural changes in phosphorylase kinase detected by small-angle X-ray scattering," Protein Science 14 (4): 1039-48 (April 2005).
M. P. Blakeley, A. J. Kalb, J. R. Helliwell, and D. A. A. Myles. "The 15-K neutron structure of saccharide-free Concanavalin A," Proceedings of the National Academy of Sciences of the United States of America 101 (47): 16405-10 (November 23, 2004).
Community genome array identifies species in natural microbial communities
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| Fluorescence images showing the improvement in array hybridization specificity with increasing temperature. Genomic DNA from an A. tolulyticus isolate Td-21 was randomly labeled with Cy5 and hybridized with CGA in the presence of 50% (v/v) formamide at 45, 55, 65, and 75°C. The hybridization signal for Td-21 genomic DNA is indicated (white arrow). Click for larger image. |
When communities of microorganisms in soil, sediment, or water are exposed to toxic contaminants or temperature changes induced by industrial practices or climate change, which species of bacteria survive these changes and which ones die out? To determine changes in the structure, composition, and adaptive responses of microbial communities, biologists need a way to identify the microorganisms dominating various communities in environmental samples. ORNL researchers have fabricated a microarray-based tool that shows promise as a highly specific, sensitive, and quantitative tool for distinguishing between different species and strains of microorganisms in environmental samples. Called a community genome array (CGA), this glass slide is dotted with labeled whole-genome "probes" that pair up, or hybridize, with "target" microorganisms of genetically identical species in natural microbial communities. CGAs may also be practical for detecting unknown microorganisms that are related genetically to bacteria known to be useful for cleaning up contaminated ecosystems. A part of this study was recently published in Environmental Science and Technology.
L. Wu, D. K. Thompson, X. Liu, M. W. Fields, C. E. Bagwell, J. M. Tiedje, and J.-Z. Zhou. "Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications, Environmental Science and Technology 38: 6775-82, 2004.
New process treats legacy radioactive wastes at lower cost
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The CSSX process. Click for larger image. |
DOE selected the caustic-side solvent extraction (CSSX) process developed at ORNL to remove radioactive cesium from alkaline nuclear waste stored at its Savannah River Site in South Carolina. The radionuclide 137Cs is present in the waste at low concentrations, yet it is responsible for a large portion of the radioactivity. It is necessary to remove the bulk of the radioactive 137Cs for safe remediation of these legacy wastes.
CSSX uses a powerful extractant that is capable of selectively removing cesium from the waste, which can include more than 10,000-fold higher concentrations of competing metal ions. The extractant is dissolved in a kerosene-based solvent; when the solvent contacts the waste, the cesium transfers from the waste to the solvent. The range of applicability of the solvent is influenced by the solubility of the extractant, which is low for the solvent now in use. A new, more soluble version of the cesium extractant prepared at ORNL has been shown to be at least eight times more soluble in the kerosene solvent, thus expanding the potential applications of the technology.
ORNL has recently developed a new process concept involving adding crown ether and carboxylic acid to the CSSX solvent that, if it proves feasible, would extend CSSX capabilities to removing both cesium and strontium in one step. This could lead to additional cost savings and waste volume reduction. Ultimately, researchers hope to develop a process to extract uranium, neptunium, and plutonium as well.
CSSX will be implemented in two ways at the Savannah River Site. The biggest application is the Salt Waste Treatment Facility, a $1 billion plant being designed by private industry to remove 99.9975% of the radioactive cesium from up to 34 million gallons of cold-war high-level-waste stored in underground tanks. CSSX is the centerpiece technology in that plant, slated to begin operation in 2010. A smaller mobile CSSX unit is being designed for implementation within the next 2 years.
Batch tests on Hanford wastes show potential for use of CSSX at Hanford, and an acid-side variant of the process may be applicable to Idaho Nuclear Engineering and Environmental Laboratory waste. The product stream from CSSX is ideal for vitrification or other end processing. Very little secondary waste is generated, and the solvent is reusable for at least a year.
Development of a domain map for nodes of the National Ecological Observatory Network (NEON)
The National Ecological Observatory Network (NEON), funded by the National Science Foundation, will be the first ecological measurement system designed both to answer regional- to national-scale scientific questions and to have the interdisciplinary participation necessary to achieve credible ecological forecasting and prediction. Capabilities provided by this infrastructural investment will transform the science of ecology by enabling the integration of research and education from natural and human systems.
A National Network Design Committee (NNDC) of 15 individuals has been tasked with providing a baseline design for NEON, including the continental-scale deployment of NEON network resources. A system of identical nodes, each representing environments within a mother geographic "domain" was envisioned. Each node would itself consist of sub-node components, and all nodes would be focused in unison on a few transformational ecological questions of national relevance.
The NNDC adopted a strategy of prestratification to help determine an optimum number of nodes and to maximize node representativeness. To better sample a phenomenon as diverse as the ecological environments of the United States, those environments were first divided into a set of more homogeneous "strata." Samples could then be arrayed within each stratum, ensuring that NEON nodes are representative of the entire range of environments within the United States.
Dr. William W. Hargrove, who serves on the NNDC, and Forrest Hoffman, both at ORNL, performed a set of statistical ecoregion analyses to assist NEON in determining the geographic domains on which the network would be based. Ecoregions have classically been used by ecologists for such national stratification. Ecoregions have historically been drawn using human expertise in a qualitative, weight-of-evidence approach. To construct NEON domains, a more transparent and repeatable process was needed.
Hargrove and Hoffman used multivariate clustering based on national maps of 9 ecologically relevant climatic "state" variables to repeatably define 25 national climatic zones. The NNDC combined these 25 climate zones with dynamic air mass seasonality data to create 20 NEON domains, each having similar climate.
Such domains are defensible in that the method used to generate them is empirical and data-driven. This analysis was also used, along with budgetary constraints, to determine the number of nodes that would be necessary to adequately sample the climatic environments within the lower 48 United States.
A preliminary version of the NEON domains map was unveiled at the August 2005 Ecological Society of America meeting in Montreal. Such domains provide the NEON design with a statistically based scientific underpinning and will make NEON the first national ecological network that has been statistically designed prior to deployment.
NEON web site: www.neoninc.org
New study shows that humic substances have a surprising influence on uranium stability and mobility
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After the bioreduction, more than 70% of reduced U(IV) in the presence of humics readily passed through 0.2-micrometer syringe filters and was oxidized to U(VI) in open air. Click for larger image. |
Humic substances, naturally forming organic materials in soil and groundwater, have been shown in past studies to promote the biological reduction and therefore immobilization of reduced uranium(IV) solid owing to its relatively low solubility. Researchers at ORNL recently discovered that, under certain conditions, the same humics can also enhance the reverse reaction; that is, they can make the precipitated solids more soluble in groundwater. This new study suggests that humics can form soluble complexes with precipitated uranium(IV) solids and that the complexes are readily oxidized upon contacting oxygen. Therefore, humics could present a challenge in maintaining the stability of uranium solids. The findings are significant because a proposed remedial strategy for contaminated soil and groundwater is predicated on the lower solubility of reduced uranium in subsurface environments.
B. Gu, H. Yan, P. Zhou, D. Watson, M. Park, and J. D. Istok. "Natural humics impact uranium bioreduction and oxidation," Environmental Science & Technology 39(14): 5268-75 (2005).
Chapter on remediation to appear in a book about perchlorate
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The field-demonstrated ORNL perchlorate treatment system using highly selective ion exchange and perchlorate destruction technologies. Click for larger image. |
Baohua Gu and Gilbert M. Brown at ORNL have written a chapter for a book about environmental perchlorate and its treatment. Dr. Gu is also one of the book's editors. The book is currently in press and will be available early 2006.
Perchlorate, a chemical mostly used in ordnance and rocket engines, poses a significant threat to human health because it disrupts thyroid function by inhibiting iodide uptake. It has recently been found to be a widespread contaminant in U.S. groundwater and surface water. This water-soluble, environmentally persistent compound now contaminates the drinking water of tens of millions of people and has been found in milk, lettuce, and many other food products in a number of supermarkets. The U.S. Environmental Protection Agency, which has reported perchlorate contamination in groundwater or surface water in more than 29 states, proposed a maximum contaminant level (MCL) of 1 ppb (µg/L) for drinking water in 2002 and recently raised the MCL to ~24 ppb on the basis of National Research Council recommendations. Cleanup costs are estimated to be in the tens of billions of dollars.
The chapter offers background on treatment strategies and describes a treatment system developed at ORNL. Prior to the work at ORNL, two treatment systems had been devised, one in which the treatment resin is used only once and another in which the resin is regenerated. Both move the perchlorate from one medium to another and thus perpetuate the waste-disposal problem. In the ORNL system, the perchlorate is trapped in a treatment bed of highly specific resin during one cycle; the resin is then regenerated and perchlorate is destroyed during a second cycle. The reaction that destroys perchlorate produces a chemical that is used to regenerate the resin, resulting in a cost reduction of up to 80% and practically zero secondary waste production.
B. Gu and G. M. Brown. "Chapter 11. Field demonstration using highly selective, regenerable ion exchange and perchlorate destruction technologies for water treatment," in Perchlorate: Environmental Occurrence, Interactions, and Treatment, ed. B. Gu and J. D. Coates, Springer (in press).
Incorporating experimental results in forest response simulations
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Experimental data inform model predictions of future climatic change. |
Accurate predictions of how eastern deciduous hardwood forests will respond to multiple environmental changes associated with climatic change are a key output for the U.S. Climate Change Science Program. Researchers at ORNL have incorporated their experimental findings from a range of field experiments-including elevated CO2, warming, precipitation change, and increased tropospheric ozone (O3)-into stand-level models to predict future responses of eastern forests in the year 2100.
Single-factor model predictions demonstrated a maximum sensitivity of eastern forests to CO2 and temperature change with minor effects from precipitation change or ozone exposure. Multi-factor simulations that ignored experimentally observed vegetation adjustments predicted a small long-term reduction in forest carbon gain by 2100. However, the opposite pattern (a 20% increase) was obtained when "lessons learned" from experimental studies were included in the analyses. Our analyses identified critical areas of uncertainty for multivariate predictions of future ecosystem response and underscored the importance of long-term field experiments for the characterization of tissue and plant acclimation and growth responses under complex environmental scenarios.
P. J. Hanson, S. D. Wullschleger, R. J. Norby, T. J. Tschaplinski, and C. A. Gunderson. "Importance of changing CO2, temperature, precipitation, and ozone on carbon and water cycles of an upland-oak forest: Incorporating experimental results into model simulations," Global Change Biology 11: 1402-23 (2005).
Subsurface contaminant research and imaging at FRC
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Coupon or “bug trap” deployed in the subsurface. Inset: microorganisms growing on media surfaces. |
Multidisciplinary teams of researchers from across the United States and overseas working at the Environmental Remediation Science Field Research Center (FRC) in Oak Ridge have shown that microorganisms found in subsurface environments can be used to reduce health risks at DOE waste sites by transforming radionuclides, such as uranium and technetium, and other contaminants into chemical forms that are less mobile or less toxic in groundwater. FRC researchers found that introducing naturally occurring humic substances (organic matter found in soil) can accelerate the chemical reduction and immobilization of these contaminants. At the same time, the researchers demonstrated that co-contaminants in the subsurface, such as nitrate, and elevated concentrations of other chemicals, like calcium, can inhibit the chemical reduction process and can reoxidize uranium, making it more mobile.
Extensive work has been conducted to identify the microorganisms present in the harsh FRC subsurface environment (an environment that is acidic and that contains high concentrations of nitrate and metals that tend to be toxic to most microorganisms). Work conducted to date has begun to determine which specific microorganisms can be used to promote the chemical reduction of radionuclides directly or indirectly. This research relies on genomic sequencing; cutting-edge techniques such as the use of functional gene arrays; and such novel devices as "bug traps," coupons that trap microbes below the ground's surface.
In addition to investigating naturally occurring microbial communities in the FRC's subsurface, researchers have developed novel geophysical, hydraulic, and tracer techniques for characterizing and monitoring subsurface processes and groundwater flow. For example, they have developed inexpensive surface geophysical techniques in which seismic waves and electrical currents are used to create three-dimensional images of the subsurface geology and of contaminated groundwater plumes. Taken together, FRC research findings have contributed to the DOE Office of Biological and Environmental Research goal of understanding the processes that influence the transport and fate of subsurface contaminants, the effectiveness and long-term consequences of extant remediation options, and the development of improved remediation strategies-especially for currently intractable contaminants or conditions. The FRC has also provided valuable opportunities to researchers engaged in genomics research. As examples, researchers associated with the Joint Genome Institute and the DOE Genomics: GTL program use FRC samples in their investigations.
D. B. Watson, W. E. Doll, T. J. Gamey, J. R. Sheehan, and P. M. Jardine. "Plume and lithologic profiling with surface resistivity and seismic tomography," Ground Water 43(2): 169-77 (2005).
J. D. Istok, 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): 468-75 (2004).
M. W. Fields, T. F. Yan, S. K. Rhee, S. L. Carroll, P. M. Jardine, D. B. Watson, C. S. Criddle, and J. Z. Zhou. "Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric acid-uranium waste," FEMS Microbiology Ecology 53(3): 417-28 (2005).
Subsurface Remedial Sciences
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Recent capping of trenches at ORNL. The contaminants were left in place. |
Soil, the thin veneer of matter covering the earth's surface and supporting a web of living diversity, is often abused through anthropogenic inputs of toxic waste. The disposal of radioactive and metal waste generated at DOE facilities within the weapons complex has historically involved shallow land burial in unsaturated soils and sediments. Disposal methods from the 1940s to the 1980s ranged from unconfined pits and trenches to single- and double-shell buried steel tanks. The scope of DOE's disposal problem is massive, with landfills estimated to contain more than 3 million cubic meters of radioactive and hazardous buried waste, a significant proportion of which has migrated into surrounding soils and groundwater. Contaminated sites are closing rapidly as a result of the demand for accelerated cleanup, and many remediation strategies have chosen to leave contaminants in place (e.g., by capping). Contaminants continue to interact with subsurface and surface media. These interactions are controlled by a complex coupling of hydrological, geochemical, and microbial processes.
A comprehensive, mission-driven science program within the Environmental Sciences Division (ESD) has been under way for the past 15 years. The program integrates ecosystem-based contaminant fate and transport processes across all scales. Our goal is to be able to understand and predict the consequences of our action or inaction with regard to contaminated environments (the consequences if buried waste is left in place or if waste leaks into the subsurface during retrieval). For example, in 2005 waste trenches were aggressively capped at ORNL. We observed a decrease in water level and the site hydraulic gradient, as well as shifts in geochemistry relative to pre-cap conditions, which suggested a local-scale influence from the cap. However, hydraulic head responses to storm events were of similar magnitude for post-cap conditions relative to pre-cap conditions, suggesting the regional-scale influence of groundwater flow and the continued discharge of contaminants from the burial grounds.
In general, experiment and numerical subsurface science research at ESD have provided knowledge and information in previously unexplored areas of fate and transport in the vadose zone (between the soil surface and the water table) to support site performance/risk assessment and decision-making processes for site restoration. Further, the research has combined DOE's commitment to environmental restoration with its commitment to major user facilities (the Stanford Synchrotron Radiation Laboratory, the Advanced Photon Source, and the Environmental Molecular Sciences Laboratory) and academic education (various universities and the Oak Ridge Institute for Science and Education).
M. A. Mayes, P. M. Jardine, T. L. Mehlhorn, B. N. Bjornstad, J. L. Ladd, and J. M. Zachara. "Hydrologic processes controlling the transport of contaminants in humid region structured soils and semi-arid laminated sediments," J. Hydrol. 275:141-61 (2003).
See More in the Highlights Archive
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