Biological and Environmental Sciences Directorate
2006 Research Highlights
The prediction of changes in carbon stocks and fluxes due to human activites is complicated by changing climate. Integrating potential carbon sequestration dynamics into the Integrated Science Assessment Model (ISAM), a coupled climate-biosphere-ocean model, allows for (a) estimates of climate change impacts on sequestration activities and (b) the separation of changes in carbon stocks occuring from purposefully implemented sequestration strategies from changes occurring due to regional weather patterns and climate change. Changes in soil carbon following a change to no-till in croplands was incorporated into the terrestrial component of ISAM. Results indicate that 5% of the soil carbon sequestered from no-till activities between 1980-2000 was caused by changes in climate. The extent to which soil C sequestration was augmented or lessened is due to soil attributes and feedbacks between climate and biophysical variables (e.g., temperature, soil moisture, decomposition rates, and changes in crop yields and residue production). Model results also indicate that an additional 3% of soil carbon accumulation in 2000 was due to previous changes in land cover (e.g., conversion of cropland to forest).
Jain, A.K., T.O. West, X. Yang, and W.M. Post. 2005. Assessing the Impact of Changes in Climate and CO2 on Potential Carbon Sequestration in Agricultural Soils. Geophysical Research Letters 32, L19711, doi:10.1029/2005GL023922.
Contact: Tris West (westto@ornl.gov)
Unique field experiment emphasizes the sensitivity of forest water use to drought
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Water is a fundamental component of the natural ecosystems upon which society depends for the delivery of vital goods and services. Water availability, although not currently a major problem in the eastern United States, could become an issue if and when changes in regional precipitation are realized. Scientists working at the Throughfall Displacement Experiment have been examining the sensitivity of deciduous forests to increases and decreases in precipitation since 1993. Sensors have been used to measure water flow in trees and scientists have related seasonal patterns of soil water potential and treatment-specific differences in forest water use to precipitation amount. Across four years in which water use was measured, there was a strong correlation between seasonal water use and the water stress integral, a cumulative index of drought severity and duration. These differences were explained by the primary effect of soil water availability on leaf and whole-plant physiology, with surprisingly little influence from drought-induced changes in canopy development, leaf area production, leaf senescence, or changes in vertical root distribution among treatment plots. Seedlings and saplings, due largely to the shallow placement of roots within the soil profile, were more sensitive to soil water availability than mature trees. Scientists conclude that while droughts in deciduous forests tend to occur late in the growing season, soil water deficits of the magnitude observed in this study have the potential to impact patterns of forest succession and local and regional forest water budgets.
Wullschleger, S.D. and P.J. Hanson. 2006. Sensitivity of canopy transpiration to altered precipitation in an upland oak forest: Evidence from a long-term field manipulation study. Global Change Biology 12: 97-109.
Contact: Stan Wullschleger (w5d@ornl.gov)
Cloud amount and surface solar radiation in China have changed significantly over the last half century
Chinese climate records obtained via a bilateral research agreement between
the US DOE and the China Meteorological Administration reveal that much of
China has experienced significant decreases in cloud cover over the last
half of the Twentieth century. This conclusion is supported by analysis of
the observed frequency of cloud-free sky and overcast sky. Total cloud cover
and low cloud cover have decreased 0.88% and 0.33% per decade, respectively,
while cloud-free days have increased 0.60% per decade, and overcast days
have decreased 0.78% per decade over China from 1954-2001. Meanwhile, both
solar radiation and pan evaporation have decreased in most parts of China,
with solar radiation decreasing 3.1 W/m2 per decade and pan evaporation decreasing
39mm per decade. Combining these results with findings of previous studies,
we postulate that increasing human-made aerosol burden (mainly SO2) has produced
a fog-like haze over much of China that has increasingly reflected and absorbed
solar radiation and resulted in less solar radiation reaching the surface,
despite concurrent decreasing trends in cloud amount and increasing trends
in cloud-free sky.
Qian, Y., D.P. Kaiser, L.R. Leung, and M. Xu. 2006. More frequent cloud-free sky and less surface solar radiation in China from 1955–2000. Geophysical Research Letters, Vol. 33, L01812, doi:10.1029/2005GL024586.
Contact: Dale Kaiser (kaiserdp@ornl.gov)
Cellular response of Shewanella oneidensis to strontium stress
The physiology and transcriptome dynamics of the metal ion-reducing bacterium
Shewanella oneidensis strain MR-1 in response to nonradioactive strontium
(Sr) exposure were investigated. Studies indicated that MR-1 was able to
grow aerobically in complex medium in the presence of 180 mM SrCl2 but showed
severe growth inhibition at levels above that concentration. Temporal gene
expression profiles were generated from aerobically grown, mid-exponential-phase
MR-1 cells shocked with 180 mM SrCl2 and analyzed for significant differences
in mRNA abundance with reference to data for nonstressed MR-1 cells. Genes
with annotated functions in siderophore biosynthesis and iron transport were
among the most highly induced (>100-fold [P< 0.05]) open reading frames
in response to acute Sr stress, and a mutant (SO3032::pKNOCK) defective in
siderophore production was found to be hypersensitive to SrCl2 exposure,
compared to parental and wild-type strains. Transcripts encoding multidrug
and heavy metal efflux pumps, proteins involved in osmotic adaptation, sulfate
ABC transporters, and assimilative sulfur metabolism enzymes also were differentially
expressed following Sr exposure but at levels that were several orders of
magnitude lower than those for iron transport genes. Precipitate formation
was observed during aerobic growth of MR-1 in broth cultures amended with
50, 100, or 150 mM SrCl2 but not in cultures of the SO3032::pKNOCK mutant
or in the abiotic control. Chemical analysis of this precipitate using laser-induced
breakdown spectroscopy and static secondary ion mass spectrometry indicated
extracellular solid-phase sequestration of Sr, with at least a portion of
the heavy metal
associated with carbonate phases.
S. D. Brown, M. Martin, S. Deshpande, S. Seal, K. Huang, E. Alm, Y. Yang, L. Wu, T. Yan, X. Liu, A. Arkin J. Zhou, D. K. Thompson. Cellular Response of Shewanella oneidensis to Strontium Stress. 2006. Appl. Environ. Microbiol. 72(1): p. 890–900.
Contacts: Steven Brown (brownsd@ornl.gov) and Dorothea Thompson (dthomps@purdue.edu)
Permeable Environmental Leaching Capsules (PELCAPs) for in situ evaluation of contaminant immobilization in soil
Spalding
and Brooks (ORNL) encapsulated radioisotope-spiked soil within a water-permeable
polyacrylamide matrix cast in a small cylindrical geometry (˜ 5 cm3)
to measure the persistence of immobilized soil contaminants. As a proof-of-principle,
soils
contained within these permeable environmental leaching capsules (PELCAPs)
were labeled with either 85Sr or 134Cs and were leached
in both laboratory tests and continuously in situ with ground and stream
waters at two field
sites on the Oak Ridge Reservation. Groups of PELCAPs were retrieved, assayed
nondestructively for radioisotopes via gamma spectroscopy, and then replaced
in ground and surface water repeatedly over a six month period. PELCAPs that
contained no soil readily and quantitatively leached either 85Sr
or 134Cs
into laboratory extractants or ground or surface water with effective diffusion
coefficients (Deff) of (1.14 ± 0.06) and (4.8 ± 0.2) × 10-6
cm2/s, respectively. PELCAPs containing thermally-treated soil
quantitatively retained both isotopes in the field tests and in laboratory
sequential extractions.
PELCAPs containing untreated soil readily leached >90% of 85Sr
but <1%
of 134Cs during field leaching at both sites. Soils were quantitatively
retained in the PELCAP polymer matrix and maintained their cation exchange
capacities
during the exposure period. Permeable polymer encapsulation methods, such
as PELCAPs, offer the potential capability to conveniently test large numbers
of soils and soil treatments for contaminant release and uptake under actual
field environmental conditions.
Spalding, B. P. and S. C. Brooks. in press. Permeable environmental leaching capsules (PELCAPs) for in situ evaluation of contaminant immobilization in soil. Environ. Sci. Technol.
Contacts: Brian Spalding (spaldingbp@ornl.gov) and Scott Brooks (brookssc@ornl.gov)
Patenting in the emerging genetic information and medical treatment industry: Access and anticommons
In May 1998, two events played pivotal roles for the emerging market for genetic information and related medical treatments. The first was a series of articles in Science magazine. These articles articulated the issues facing the U.S. Patent and Trademark Office (USPTO) in determining which patents should issue among the then-rapidly growing backlog of applications for gene sequence discoveries and related information.
The second event of significance that May was the formation of Celera Corporation. Celera’s mission was to sequence the human genome at breakneck pace using new technologies. In doing so, Celera challenged the Federal program to a “race” wherein the finish line would demarcate the complete identification of the base genome—the genetic code of the “representative human.” Fueled by the hubris of the late 1990s, the emergence of new gene sequencing technology, and the potential for immense corporate gains, Celera confronted the fundamental basis for public support of basic research—the belief that private dollars would not support basic inquiry because investments could not be recovered in the market place. Celera was wagering that, through a combination of patents and data base tools, it could profit from what was previously considered basic research.
This paper, “Patenting in the Emerging Genetic Information and Medical Treatment Industry,” traces the development of patenting and other public policy issues accompanying the build-up in biotechnology research. It first reviews the interplay between patent policy and genomic technology between 1998 and 2001, when the base genome was published. Following this review, it examines results from several studies that seek to identify instances where anticommons behavior is evident or when access to needed information has been blocked. The studies report that there is little evidence that intellectual property rights restrictions have seriously inhibited the ability of companies or university to carry out planned research. However, we believe that the evidence is far too thin to support a general conclusion that patenting issues have been overcome because the potential profits from biomedical practices have been limited to date. As these potential profits grow, we conclude that patenting issues will also grow in importance.
David J. Bjornstad and Christine Dummer, “Patenting in the Emerging Genetic Information and Medical Treatment Industry,” ICFAI Journal of Intellectual Property Rights, August 2005, pp. 19-31.
Contact: David J. Bjornstad (bjornstaddj@ornl.gov)
Artificial neural networks allow researchers to relate groundwater geochemistry to microbial community structure
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Sensitivities of geochemical variables in predicting PLFA classes with the median-performing NN model. A larger sensitivity value indicates that the PLFA abundance is more sensitive to small changes in the concentration of the corresponding geochemical variable. |
Nonlinear and generalized linear data analysis methods were applied to relate microbial biomarkers (phospholipids fatty acids [PLFA]) to groundwater geochemical measurements at the Shiprock New Mexico uranium mill tailings disposal site that is contaminated primarily by uranium, sulfate, and nitrate. Feedforward artificial neural network (NN) models were used to predict PLFA classes from geochemistry. To reduce the danger of model overfitting, parsimonious NN architectures were selected based on elimination of redundant predictor (geochemical) variables and pruning of hidden nodes. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPCs grouped the samples according to similar geochemistry. PLFA indicators of gram negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The PLFA data also indicated that the more contaminated samples contained microbial communities that were predominated are indicative of metal-reducers, actinomycetes, and gram positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.
Jack C. Schryver, Craig C. Brandt, Susan M. Pfiffner, Anthony V. Palumbo, Aaron D. Peacock, David C. White, James P. McKinley, and Philip E. Long (2006) Application of Nonlinear Analysis Methods for Identifying Relationships Between Microbial Community Structure and Groundwater Geochemistry, Microbial Ecology, in press
Contact: Craig C. Brandt (brandtcc@ornl.gov)
Hydropower without dams: The potential for hydrokinetic and wave energy technologies
Compared to conventional hydropower facilities (which typically require the
construction of dams, powerhouses, and reservoirs), free-flow turbines are
expected to have much smaller impacts on survival and migrations of fish,
aquatic and terrestrial habitats, water quality, sediment transport, and
visual/aesthetic qualities. DOE recently sponsored a workshop1 that brought
experts together to discuss the characteristics of hydrokinetic and wave
energy technologies, the appropriate environments for deployment, environmental
concerns associated with deployment, and needed research and mitigation.
With support from State Partnership Program funding, ORNL staff provided
technical assistance to the New York State Energy Research and Development
Agency and the developer of a submerged, free-flow turbine array in the East
River, New York City on methods to evaluate the potential for injury to fish
and other aquatic animals from contact with the rotating blades. Guidance2
on how to deal with these issues has been published to help developers and
regulators understand the environmental issues surrounding these new technologies.
Although much can be learned from studies of conventional turbines, there
is a fundamental concern about extrapolating the environmental effects from
single units to energy farms comprised of dozens or hundreds of hydrokinetic
turbines.
1U.S. Department of Energy 2006. Proceedings of the
Hydrokinetic and Wave Energy Technologies Technical and Environmental
Issues
Workshop. October 26-28, 2005. Washington, DC.
2Coutant, C.C. and G.F. Cada 2005. What’s the Future of
Instream Hydro? Hydro Review XXIV(6):42-49.
Contact: Glenn F. Cada (cadagf@ornl.gov)
Ecosystem models may help forecast coastal forest recovery following hurricanes
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Predicted tree wood biomass (AGWB), soil N (SOILN), soil C (SOC), and potential excess soil N (PEN) under different regimes of prescribed burning. Sustainable ecosystem recovery after forest thinning is illustrated by line “A” and unsustainable recovery after clear-cutting is illustrated by line “B”. |
Hurricanes can have widespread impacts on upland forest resources of coastal regions in the southeastern US, leaving forest stands in need of restoration and/or rehabilitation. However, little is currently known about how various measures of soil quality affect the potential for post-disturbance forest recovery and how various post-disturbance management practices affect the sustainability of recovering ecosystems on sandy, nutrient-poor soils. Recent research on military installations, by the Environmental Sciences Division (ORNL), has addressed ways of forecasting soil quality thresholds to ecosystem recovery following disturbance and predicting the effect of common land management practices (like prescribed burning and harvesting) on forest sustainability. The research suggests that measurements of soil carbon and nitrogen can be used to define thresholds to ecosystem recovery and that nutrient limitation can be a key constraint on the recovery and sustainability of desired future ecosystem conditions following forest disturbance on the southeastern coastal plain.
Garten, C.T., Jr., Ashwood, T.L., 2004. Modeling soil quality thresholds to ecosystem recovery at Fort Benning, GA, USA. Ecological Engineering 23: 351-369.
Garten, C.T., Jr., 2006. Predicted effects of prescribed burning and harvesting on forest recovery and sustainability in southwest Georgia, USA. Journal of Environmental Management (in press).
Contact: C.T. Garten, Jr. (gartenctjr@ornl.gov)
Genetic individual-based population model evaluates demographic benefits and genetic costs of hatcheries
H.I. Jager (ORNL) developed a genetic individual-based model of white sturgeon
(Acipenser transmontanus) populations in a river to examine the genetic
and demographic
trade-offs associated with operating a conservation hatchery. Simulation
experiments evaluated three management practices: (1) setting quotas to
equalize family contributions in an effort to prevent genetic swamping,
(2) an adaptive management scheme that interrupts stocking when introgression
exceeds a specified threshold, and (3) alternative broodstock selection
strategies that influence domestication. Results recently published in the
Canadian Journal of Fisheries and Aquatic Sciences challenge two common
suppositions about aquaculture practices.
Genetic swamping: The first set of simulations, designed to evaluate equalizing the genetic contribution of families, did not show the genetic benefits expected. Maximum allele frequency, a measure of swamping, did not increase significantly with an increase in the quota of hatchery juveniles released from each family. Furthermore, this practice led to smaller final simulated populations. However, the practice would guard against selection for traits that are beneficial in a hatchery environment.
Introgression: The second set of simulations showed that simulated adaptive management was not successful in controlling introgression over the long term, especially with uncertain feedback from survey data.
Domestication: The third set of simulations compared the effects of three alternative broodstock selection strategies on domestication for hypothetical traits controlling early density-dependent survival. Simulated aquaculture selected for a density-tolerant phenotype when broodstock were taken from a genetically connected population. Using broodstock from an isolated population (i.e., above an upstream barrier or in a different watershed) was more effective at preventing domestication than using only wild broodstock from a connected population.
Jager, H.I. 2005. Genetic and demographic implications of aquaculture in white sturgeon (Acipenser transmontanus) conservation. Canadian Journal of Fisheries and Aquatic Sciences 62: 1733-1745.
Contact: H.I. Jager (jagerhi@ornl.gov)
Insect infestations linked to shifts in microclimate: Important climate change implications
Climatic change assessments and models tend to focus on how large-scale alterations
in climate may alter vegetation. However, a major challenge in dealing with
climatic change effects now and in the future is trying to predict the secondary
and cascading effects in ecosystems. Vegetation not only responds to changes
in climate but also creates distinct microclimate patterns; ecosystem processes
are affected by both the general climate and by these microclimate patterns.
Insect outbreaks are predicted to increase with climate change and can cause
rapid changes in vegetation with concomitant changes in microclimate. Understanding
how herbivores indirectly alter the soil microclimate will enable scientists
to make better predictions about how to manage systems under changing climatic
regimes.
Classen AT, Hart SC, Whitham TG, Cobb NS, Koch GW. 2005. Insect infestations linked to shifts in microclimate: important climate change implications. Soil Science Society of America Journal 69:2049-2057.
Contact: Aimee Classen (classenat@ornl.gov)
Forest productivity increases in a CO2-enriched atmosphere: A synthesis of FACE experiments
Climate change predictions from models are highly dependent on assumptions
about feedbacks between the biosphere and atmosphere. One critical feedback
occurs if C uptake by the biosphere, or its net primary productivity (NPP),
increases in response to the fossil-fuel driven increase in atmospheric [CO2]
(“CO2 fertilization”), thereby slowing the rate of increase in
atmospheric [CO2]. We analyzed the response of NPP to elevated CO2 (~550
ppm) in four free-air CO2 enrichment (FACE) experiments in forest stands.
We show that the response of forest NPP to elevated [CO2] is highly conserved
across a broad range of productivity, with a stimulation at the median of
23 ±2%. The surprising consistency of response across diverse sites provides
a benchmark to evaluate predictions of ecosystem and global models and allows
us now to focus on unresolved questions about carbon partitioning and retention,
and spatial variation in NPP response caused by availability of other growth
limiting resources.
Norby RJ, DeLucia EH, Gielen B, Calfapietra C, Giardina CP, King JS, Ledford J, McCarthy HR, Moore DJP, Ceulemans R, De Angelis P, Finzi AC, Karnosky DF, Kubiske ME, Lukac M, Pregitzer KS, Scarascia-Mugnozza GE, Schlesinger WH, Oren R. 2005. Forest response to elevated CO2 is conserved across a broad range of productivity. Proceedings of the National Academy of Sciences (in press).
Contact: Richard Norby (rjn@ornl.gov)
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