Evaluating the Efficacy of Evaluating the Efficacy of Bioremediation of Uranium Bioremediation of Uranium in the Subsurface in the Subsurface Philip E. Long Pacific Northwest National Laboratory Federal Remediation Technologies Roundtable 15 November 2007 EPA Conference Center, Arlington, VA
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Evaluating the Efficacy of Evaluating the Efficacy of Bioremediation of Uranium Bioremediation of Uranium in the Subsurfacein the Subsurface
Philip E. Long
Pacific Northwest National Laboratory
Federal Remediation Technologies Roundtable15 November 2007 EPA Conference Center, Arlington, VA
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Outline of presentationOutline of presentationOutline of presentation
Background: persistence of uranium groundwater plumesConcept for uranium bioremediationApproach to development of a mechanistic understanding of subsurface mobility of uranium at the field scaleEvaluation of uranium bioremediationFuture directions and developments
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Persistence of uranium groundwater plumes (U(VI) Concentrations (mg/L))
Persistence of uranium groundwater plumesPersistence of uranium groundwater plumes (U(VI) Concentrations (mg/L))(U(VI) Concentrations (mg/L))
Presenter�
Presentation Notes�
At the Old Rifle site, uranium (~1-2uM) is the risk driver for the site and is present at low but significant concentrations across the site, particularly in the subsurface beneath where the spent ore tailings were piled. Our test site is located within the area of high(er) concentrations of uranium in the groundwater. The subsurface is dominated by braided deposits of sand and coarse gravels and cobbles. Depth to the confining layer is approximately 20 ft. Saturated aquifer thickness is about 12ft. The site is naturally anoxic with abundant Fe(II) in the sediments, occasional spikes in nitrate concentration and low DO near the water table. The current remediation decision for the site is natural flushing. �
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Well 655
Persistence of uranium groundwater plumes (U(VI) Concentrations (mg/L))
Persistence of uranium groundwater plumesPersistence of uranium groundwater plumes (U(VI) Concentrations (mg/L))(U(VI) Concentrations (mg/L))
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Concept for U(VI) bioreductionConcept for U(VI) Concept for U(VI) bioreductionbioreduction
U(VI) is the mobile valence state of uraniumReduced uranium, U(IV), is insoluble as uraniniteReduction of U(VI) to U(IV) within aquifers could precipitate and immobilize uraniumLab studies suggest simple strategy to promote U(VI) reduction in contaminated aquifers:
add acetate as an electron donor to stimulate dissimilatory metal-reducing microorganismsU(VI) is reduced concurrently with Fe(III)
C CC C
Fe(II)
CO2
e-
Fe(III)
U(VI)
U(IV)U(IV)
C CH3
O−ONa+
Acetate structureLactate structure
• Typical human hair diameter:100,000 nanometers (nm)• Geobacter cell at left 300 nm wide• “Nanowires” ~10 nm(image from Reguera et al. Nature Vol 435, 23 June 2005)
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Implementation of in situ bioremediation of U(VI)
Implementation of Implementation of in situin situ bioremediation bioremediation of U(VI)of U(VI)
Acetate Solution(Low Conc.)DO < 1mg/L
N2
InjectionGallery
Pump or Gravity feed
Acetate
GroundwaterFlow
CH3COO-
CH3COO-
CH3COO-
CH3COO-
CH3COO-
CO2
Fe(III)Fe(II)
CH3COO-
U(VI)U(IV)
U(VI)U(VI)
U(VI)
U(VI)U(VI)
U(VI)
U(VI)
U(VI) U(VI)
U(VI)
U(VI)
Zone of U(VI) Removal}
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Context for metal and radionuclide bioremediation
Context for metal and radionuclide Context for metal and radionuclide bioremediationbioremediation
Context for field bioremediation research at the Old Rifle Uranium Mill Tailings Site Context for field bioremediation research Context for field bioremediation research at the Old Rifle Uranium Mill Tailings Siteat the Old Rifle Uranium Mill Tailings Site
Presenter�
Presentation Notes�
The Old Rifle Site is one of these uranium ore extraction facilities. The site is located in the town of Rifle just off of I-70 on the Western slope of Colorado. The tailings pile, extraction facilities, ore storage areas, basically most surface structures and stored materials have since been removed from the site in accordance with Uranium Mill Tailings Remedial Action program. The top 4 to 7 feet of surface soil was also removed and a clay cap put into place prior to re-soiling and planting. Our test plot is located within an area of site where the spent tailings were stored.�
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11
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Conceptualized Test Plot
Observation wellsControl Wells
Injection Gallery Detail
Acetate
GW flow
25 ft
50 ft
80 ft
Injection Gallery
1ft
5ft
B-01
0.00.20.40.60.81.01.21.4
B-02
0.00.20.40.60.81.01.21.4
B-03
Days
0 20 40 60 80 1000.00.20.40.60.81.01.21.4
M-01
0.00.20.40.60.81.01.21.4
M-02
0.00.20.40.60.81.01.21.4
M-03
0.00.20.40.60.81.01.21.4
M-04
0.00.20.40.60.81.01.21.4
M-05
0 20 40 60 80 1000.00.20.40.60.81.01.21.4
M-06
0.00.20.40.60.81.01.21.4
M-07
0.00.20.40.60.81.01.21.4
M-08
0.00.20.40.60.81.01.21.4
M-09
0.00.20.40.60.81.01.21.4
M-10
0 20 40 60 80 1000.00.20.40.60.81.01.21.4
M-11
0.00.20.40.60.81.01.21.4
M-12
0.00.20.40.60.81.01.21.4
M-13
0.00.20.40.60.81.01.21.4
M-14
0.00.20.40.60.81.01.21.4
M-15
0 20 40 60 80 1000.00.20.40.60.81.01.21.4
U(VI) (uM)
Previous work at the Rifle SitePrevious work at the Rifle SitePrevious work at the Rifle Site
CFBfirmicutesbetaactinobacteriaSpirochetesDesulfosporosinusotherVerrumicrobiaother deltaSO4 Red - deltaGeobacteraceae
18 24 39
Days Since Beginning Acetate Injection%
16S
rDN
Ase
quen
ces
240%
20%
40%
60%
80%
100%
Background M-07
Presenter�
Presentation Notes�
Research at the site has focused on stimulating the in situ activity of metal-reducing microorganisms in the subsurface to reduce and immobilize uranium from the groundwater at this site. This has been accomplished through the installation of injection galleries upgradient of a series of monitoring wells. Acetate is injected into the aquifer over time and changes in the subsurface are monitored via groundwater and sediment sampling in and among the downgradient monitoring wells. In all tests geochemical data has been collected in concert with advanced molecular biology techniques to link changes in geochemistry with changes in microbial community composition. This approach will be emphasized even further under the new IFC and will also be linked with geophysical changes detected in the subsurface. �
U(VI) loss for both 2002 and 2003 U(VI) loss for both 2002 and 2003 experimentsexperiments
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0
10
20
30
40
50
60
70
80
90
100
May 20
02Ju
ne 20
02Ju
ly 20
02
Augus
t 200
2
Septem
ber 2
002
Octobe
r 200
2
Novem
ber 2
002
Decem
ber 2
002
June
2003
July
2003
Augus
t 200
3
Septem
ber 2
003
Octobe
r 200
3
Novem
ber 2
003
Janu
ary 20
04
Februa
ry 20
04Marc
h 200
4Apri
l 200
4May
2004
June
2004
July
2004
Novem
ber 2
004
Februa
ry 20
05Apri
l 200
5Ju
ne 20
05
Decem
ber 2
005
Septem
ber 2
006
Decem
ber 2
006
% U
(VI)
Rem
aini
ng
2002 Acetate
Amendment
2003 Acetate
Amendment
The Unexpected Continued Removal of U(VI)
U(VI) loss between B02 and M08
The Unexpected Continued Removal of U(VI)The Unexpected Continued Removal of U(VI)
U(VI) U(VI) loss between B02 and M08loss between B02 and M08
Source: N’Guessan et al. 2007 ES&T in review
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Firmicutes predominate in post-amendment reduced sediment
Distribution of 16S rRNA gene sequences
FirmicutesFirmicutes predominate in postpredominate in post--amendmentamendment reduced sedimentreduced sediment
Distribution of 16S Distribution of 16S rRNArRNA gene sequencesgene sequences
Source: N’Guessan et al. 2007 ES&T in review
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Passive multilevel samplers. A. Cell on support rod being lowered into monitoring well. B. MLS cells from a background well. C. MLS cells from a treatment zone well undergoing sulfate reduction.
A. B.
C.
Rifle Integrated Field Challenge Site:Rifle Integrated Field Challenge Site:Rifle Integrated Field Challenge Site:Objective: development of a mechanistic understanding of subsurface mobility of uranium at the field scaleTesting hypotheses relating to:
Extension of Fe-reducing conditionsU(VI) Sorption under reducing conditionsMechanisms for post-biostimulation U removalRates of natural bioreduction of U
Key approaches:Mechanisms of U bioreduction illuminated by protein expressionRelative contribution of biotic processes and abiotic uranium immobilization processes evaluated (e.g. U bioreduction and U sorption)Correlation of subsurface geochemical processes with geophysical monitoring of subsurface redox status associated with bioreductionComprehensive reactive transport modeling of uranium mobility in the subsurface
Presenter�
Presentation Notes�
The overall science themes for the Old Rifle IFC build on and extend earlier research observations and incorporate new techniques into the research plan. For example: we will attempt to deploy proteomics techniques to monitor stimulated subsurface microbial communities during metal reduction in a testable format. These data will be closely coupled with gene expression, genomic and community sequencing efforts to provide the most cutting edge description of microbial community dynamics yet attempted in subsurface environments. We will evaluate the major immobilization processes for uranium in detail to assess the relative importance of enzymatic reduction, sorption, mineralization and the potential, if any, for abiotic uranium reduction. We will examine stimulated changes in subsurface processes (TEAPs) and correlate these observations with geophysical measurements taken at the surface in order to evaluated new noninvasive ways of monitoring uranium bioremediation from the surface. Also, we will incorporate the collected data into a comprehensive reactive transport model for the site that should provide not only a better accounting of the major factors affecting uranium mobility at this UMTRA site but also a simulation of in situ metal reduction and uranium bioremediation. �
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2007 field experimentReplicated earlier field experiments showing U(VI) bioreductionby GeobacterIntentionally limited acetate during part of the experimentSuccessfully generated samples for proteomic and metagenomic analysis Data sets include: U(VI) removal rates, hydraulic conductivity, hydrogeophysical monitoring, gene expression data, mineralogical changes, in situ incubators/sensorsDirect access to naturally bioreduced sediment (and uranium?)
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Winchester Well Layout and Distribution of Reduced Sediments
Winchester Well Layout and Distribution of Winchester Well Layout and Distribution of Reduced SedimentsReduced Sediments
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Fe(II) and U(VI) trendsFe(II) and U(VI) trendsFe(II) and U(VI) trends
Uranium Concentration (μM) as a function of time (days)Uranium Concentration (Uranium Concentration (μμM) as a function of time (days)M) as a function of time (days)
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Proteomic Sampling and Characterization of the Microbial Community Structure and Dynamics During Electron Donor Amendment at the Rifle IFC
• In groundwater from downgradient wells, proteins from six different Geobacter species were detected where G. bemidjiensis was the most abundant organism•Protoemic data are also being used to characterize the microbial community from stimulated sediments•Proteomic data are being obtained both at EMSL/PNNL and ORNL, and analyzed jointly with UC Berkeley
High throughput 9.4 Tesla FTICR(PNNL/EMSL)
FT-MS Orbitrap(ORNL)
Tangential Flow Filtration (TFF) U Mass
G. m
etal
lired
ucen
s
s i s 2 s s
S a m p l e s e t 1 ( 8 / 1 7 D - 0 ? )S a m p l e s e t 2 ( 8 / 2 3 D - 0 5 )
G. b
emid
gien
sis
G. l
ovle
yi
G. s
p_FR
C_3
2
G. s
ulfu
rred
ucen
s
G. u
rani
umre
duce
ns
Pro
tein
s
0
100
200
300Well D-07 (8/17/07)Well D-05 (8/23/07)
Presenter�
Presentation Notes�
SBY: At some point, you have to make the case for doing the proteomics – you might focus on the uniqueness of site-specific conditions with regard to one-size does not fit all �
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Evaluation of uranium bioremediationEvaluation of uranium bioremediationEvaluation of uranium bioremediation
CharacterizationConceptual model developmentMonitoringNumerical modeling
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CharacterizationCharacterizationCharacterization
Importance of Sediment Grain Size to U sorptionImportance of Sediment Grain Size to U sorptionImportance of Sediment Grain Size to U sorption
Uranium 0.5 M Nitric Acid Extractions for "D-08 16"
0.000
2.000
4.000
6.000
8.000
10.000
12.000
14.000
16.000
18.000
20.000
< 53
micr
on
<106
> 53
micr
on
< 149
> 1
06 m
icron
< 250
> 1
49 m
icron
< 500
> 2
50 m
icron
< 100
0 > 5
00 m
icron
<2000
>10
00 m
icron
<2000
micr
on
Grain Size Fraction
U c
onc e
ntra
tion
(μg/
gse
d im
ent)
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MonitoringMonitoringMonitoring
Seasonal changesAppropriate spatial coverageReal time monitoringEvent-based samplingPassive in situ geochemical and biological sampling
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2002 2003 2004 2005 2006
Water Table Elevation, Rifle Site 2001 to 2006
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Stratified Water ChemistryStratified Water ChemistryStratified Water Chemistry
Depth-dependent U(VI) and DOHighest DO and U(VI) near the water tableIssues
Oxygen diffusion through water tableBackground utilization of DOScreened interval of wells
Reactive Transport Modeling of Uranium Bioreduction
Reactive Transport Modeling of Uranium Reactive Transport Modeling of Uranium BioreductionBioreduction
Initial aqueous U(VI) spatially variable Initial timing of aqueous U(VI) removal reproduced by model Uranium rebound is slower than model prediction Considerations
Sulfate reducers removing some uranium Uranium adsorption retarding front
Row 1
Row 2
Row 3
Exploring effects of physical and chemical heterogeneities on spatial patterns of calcite precipitation
Homo conductivity Homo solid Fe field
Hetero conductivity Homo solid Fe field
All three cases: same average flow velocity, and same total solid iron contentHeterogeneous conductivity field obtained from inverse modeling of tracer dataHeterogeneous Fe content: negative correlation with conductivity
Hetero conductivity Hetero solid Fe field
Physical and chemical heterogeneities lead to locally larger amounts of calcite precipitation, therefore increases the possibility of clogging.
Carl Steefel, Li Li (LBNL)
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Future directions and developmentsFuture directions and developmentsFuture directions and developments
In-field monitoring of selected genes and proteinsCoupling of reactive transport models with in silico microbial models
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Field Portable Microarray Analysis of Groundwater and Sediment
Field Portable Field Portable MicroarrayMicroarray Analysis of Analysis of Groundwater and SedimentGroundwater and Sediment
ERSP ScienceERSP Science
• Breadboard lab instrument
• Automated methods for direct detection of RNA
• Environmentally relevant samples, biomass and sample sizes
• Environmentally relevant and vetted microarray probes
• Statistical techniques for converting noisy data into actionable information
Will isolate both DNA and RNA simultaneouslySimultaneous asymmetric amplification + microarray hybridization in same flow cell (120 min)
Single-pot DNA or RNA amplification and labelingWash (5 min)Imaging, data extraction, analysis and reporting (5 min)= 2.5 hours, sample-to-answer microbial community profiling
Rifle site
Sample Prep
Array
Community Profiles
Responsive organisms
+
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Constraint-Based In Silico ModelingConstraintConstraint--Based Based In In SilicoSilico ModelingModeling
Genetic characterization of reaction pathwaysLaboratory characterization of flux constraintsOptimization under specific conditions
Biological Information
Understand Metabolism
In silico Cellular Models
Predict Growth Physiology
Analyze high-throughput data
Slide material from R. Mahadevan (Univ. of Toronto)
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Conclusions on U(VI) bioremediation (natural gradient, non-displacive)
Conclusions on U(VI) bioremediation Conclusions on U(VI) bioremediation (natural gradient, non(natural gradient, non--displacivedisplacive))
Effectively removes U(VI) from groundwaterAdditional field-scale research needed understand mechanisms and durabilityPrecise monitoring of microbial activity on the horizonElectron donor pulsing and “engineering” of specific precipitates in situ may enhance long-term stabilityCompatible with monitored natural attenuationAmenable to regulatory evaluation
AcknowledgementsAcknowledgementsAcknowledgementsFunding for documenting the prerequisite characterization, conceptual model requirements, and monitoring requirements is provided by the U.S. Nuclear Regulatory CommissionFunding for all three IFC’s (Rifle, CO, Hanford 300 Area, and ORNL) is provided by the U.S. Department of Energy, Office of Science, Biological and Environmental Research, Environmental Remediation Sciences DivisionPacific Northwest National Laboratory is operated by Battelle Memorial Institute for the United States Department Of Energy under Contract DE-AC06-76RL01830
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Rifle IFC Project ParticipantsRifle IFC Project ParticipantsRifle IFC Project ParticipantsJ. Banfield2, R. Bush3, K. Campbell4, D.P. Chandler5, J.A. Davis4, R. Dayvault6, J. Druhan2, H. Elifantz7, A. Englert8, R. L. Hettich9, D. Holmes7, S. Hubbard8, J. Icenhower1, P.R. Jaffe10, L.J. Kerkhof11, R.K. Kukkadapu1, E. Lesher12, M. Lipton1, D. Lovley7, S. Morris6, S. Morrison6, P. Mouser7, D. Newcomer1, L. N’Guessan7, A. Peacock13, N. Qafoku1, C. T. Resch1, F. Spane1, B. Spalding9, C. Steefel8, N. VerBerkmoes9, M. Wilkins2, K.H. Williams8, S.B. Yabusaki1
1. Pacific Northwest National Laboratory, Richland, WA 988162. University of California, Berkeley; Berkeley, CA 947203. Legacy Management, U.S. Department of Energy, Grand Junction, CO 815034. U.S. Geological Survey, Menlo Park, CA 940255. Akonni Biosystems, Frederick, Maryland 21701 6. SM Stoller, Inc., Grand Junction, CO 815037. Department of Microbiology, University of Massachusetts, Amherst, MA 010038. Lawrence Berkeley National Laboratory, Berkeley, CA 947209. Oak Ridge National Laboratory, Oak Ridge, TN 3783010.Dept. of Civil and Environmental Engineering, Princeton University, Princeton, NJ
0854411.Institute of Marine and Coastal Sciences, Rutgers University, Brunswick, NJ 0890112.Division of Environmental Science and Engineering Colorado School of Mines,
Golden, CO 8040113.Microbial Insights, Inc., Rockford, TN 37853