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SUPPLEMENTARY INFORMATIONdoi: 10.1038/ngeo589
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Supplementary information for
Storage and bioavailability of molybdenum in soils
increased by organic matter complexation
Thomas Wichard 1,¶ , Bhoopesh Mishra 1,¶,*, Satish C.B. Myneni1, Jean-Philippe
Bellenger1 and Anne M.L. Kraepiel 1,2
Princeton University, Department of Geosciences1 and Chemistry Department2,
Guyot Hall, Princeton, NJ 08544, USA
¶ Joint first authorship
To whom correspondence should be addressed:
* email: [email protected]
Content:
1. Methods
2. Supporting Tables
3. Supporting Figures
4. Acknowledgements
5. References
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Methods
Chemicals.
Cysteine, malic acid (2-hydroxybutanedioic acid), tannic acid (C76H52O46) and sodium
molybdate were purchased from Sigma-Aldrich and used without further purification.
Azotochelin (L-LysineCAM) and azotobactin were prepared as previously
described15,20,30.
Collection and preparation of soil samples.
Mo-rich soil samples were collected from an exposed soil profile in the Red mountain of
the Coronado National Forest (AZ, USA) and directly analyzed using µXRF mapping
and µXANES spectroscopy.
Topsoil and subsoil samples were separated from a 0.5 m core collected from a hardwood
forest in central New Jersey (USA). For each sample, 1 g of the sieved soil was mixed
with 10 ml of a 0.2 mM aqueous solution of Na2MoO4. After 24 h, the soil suspension
was filtered (GF, pore size 0.45 µm, Whatman, UK), and the collected soil particles were
analyzed by XANES spectroscopy. Measurement of Mo concentration in the filtrate
showed that 31-43% of the added molybdate was bound to the soil particles.
Preparation of the leaf organic matter extract (LL).
Leaf litter from a mixed stand of maple and oak trees in the Pine Barrens (NJ, USA) was
collected, air-dried and ground with a mortar and pestle. The ground leaves were
extracted with distilled water (1:10 (w/w) dry leaf to water ratio) at 24̊ C for 24 h 31. The
resulting suspension was filtered through a glass fiber filter (GF, pore size 0.45 µm,
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Methods
Chemicals.
Cysteine, malic acid (2-hydroxybutanedioic acid), tannic acid (C76H52O46) and sodium
molybdate were purchased from Sigma-Aldrich and used without further purification.
Azotochelin (L-LysineCAM) and azotobactin were prepared as previously
described15,20,30.
Collection and preparation of soil samples.
Mo-rich soil samples were collected from an exposed soil profile in the Red mountain of
the Coronado National Forest (AZ, USA) and directly analyzed using µXRF mapping
and µXANES spectroscopy.
Topsoil and subsoil samples were separated from a 0.5 m core collected from a hardwood
forest in central New Jersey (USA). For each sample, 1 g of the sieved soil was mixed
with 10 ml of a 0.2 mM aqueous solution of Na2MoO4. After 24 h, the soil suspension
was filtered (GF, pore size 0.45 µm, Whatman, UK), and the collected soil particles were
analyzed by XANES spectroscopy. Measurement of Mo concentration in the filtrate
showed that 31-43% of the added molybdate was bound to the soil particles.
Preparation of the leaf organic matter extract (LL).
Leaf litter from a mixed stand of maple and oak trees in the Pine Barrens (NJ, USA) was
collected, air-dried and ground with a mortar and pestle. The ground leaves were
extracted with distilled water (1:10 (w/w) dry leaf to water ratio) at 24̊ C for 24 h 31. The
resulting suspension was filtered through a glass fiber filter (GF, pore size 0.45 µm,
3
Whatman, UK) and the filtrate yielded the extract of leaf organic matter (leaf litter
extract, LL) that was subsequently frozen. In one experiment, a subsample of LL was
stored in the laboratory at 24̊ C for one month to evaluate the stability of the Mo -binding
groups over time. The polyphenol concentration of LL was estimated using the
colorimetric assay of Denis-Folin, and found to be equal to 1.3 × 10-2 M (expressed as
2,3-dihydroxybenzoic acid equivalents31,32). For XANES and EXAFS spectroscopy, LL
subsamples were spiked with an aqueous solution of Na2MoO4 to achieve a final Mo
concentration of 1 mM. To study the effect of pH on Mo binding to LL, the pH of the leaf
extract was adjusted with 0.1 N NaOH.
Chemical composition of the soils.
All soils were sieved, ground (fine grade) and dried at 90˚C for two days. Soil carbon and
nitrogen were measured on a 0.4 g subsample using a dry-combustion LECO analyzer
(LSU AgCenter, LA, USA). For determination of metal concentrations, about 50-100 mg
of dried leaf litter or soil samples were weighted and subsequently pre-digested in 8 ml of
nitric acid (68%, trace metal clean grade, Fisher Scientific, USA) for 24 h at 60˚C. The
samples were then digested in a MARS Xpress Microwave digester (CEM) and their
concentrations in Fe, and Mo were measured with an Inductively Coupled Plasma-Mass
Spectrometer (ICP-MS, Element2, Thermo Finnigan) at medium resolution.
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Mo adsorption on iron oxides.
Goethite (α-FeOOH), hematite (α-Fe2O3) and ferrihydrite (Fe5HO8 ∙ 4H2O) were freshly
prepared according to established procedures33. The resulting iron oxides were collected
by filtration, rinsed with water and dried at 90°C.
To study Mo adsorption, 0.5 g of iron oxide was incubated in 10 ml of a 1.0 M aqueous
solution of Na2MoO4 at 24˚C for 24 h. The pH was adjusted to 4.5 ± 0.2 with 0.1 M HCl
and measured again after 24 h (∆pH = 0.05). The resulting solid was collected by
centrifugation, rinsed with 15 ml water and air-dried before analysis by XANES
spectroscopy.
Preparation of Mo-tannic acid complex.
Addition of an excess of an aqueous solution of Na2MoO4 (0.5 M final concentration) to
a 0.1 M solution of tannic acid in methanol resulted in the formation of a precipitate12,
which was filtered, washed and subsequently air-dried. Complete complexation of Mo by
tannic acid in the precipitate was demonstrated by EXAFS spectroscopy and ultraviolet-
visible spectroscopy.
Preparation of Mo-cysteine complexes.
Orange crystals of di−µ−oxo-bis-{oxo[cysteinato(2-)]aquo-molybdate (V)} trihydrate
were prepared from aqueous solutions of molybdenum(VI) and cysteine following
published procedures28,34 . The Mo(VI) complex forms first, and is reduced to Mo(V)
complexes over time in aqueous solution with an excess of cysteine35.
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Mo adsorption on iron oxides.
Goethite (α-FeOOH), hematite (α-Fe2O3) and ferrihydrite (Fe5HO8 ∙ 4H2O) were freshly
prepared according to established procedures33. The resulting iron oxides were collected
by filtration, rinsed with water and dried at 90°C.
To study Mo adsorption, 0.5 g of iron oxide was incubated in 10 ml of a 1.0 M aqueous
solution of Na2MoO4 at 24˚C for 24 h. The pH was adjusted to 4.5 ± 0.2 with 0.1 M HCl
and measured again after 24 h (∆pH = 0.05). The resulting solid was collected by
centrifugation, rinsed with 15 ml water and air-dried before analysis by XANES
spectroscopy.
Preparation of Mo-tannic acid complex.
Addition of an excess of an aqueous solution of Na2MoO4 (0.5 M final concentration) to
a 0.1 M solution of tannic acid in methanol resulted in the formation of a precipitate12,
which was filtered, washed and subsequently air-dried. Complete complexation of Mo by
tannic acid in the precipitate was demonstrated by EXAFS spectroscopy and ultraviolet-
visible spectroscopy.
Preparation of Mo-cysteine complexes.
Orange crystals of di−µ−oxo-bis-{oxo[cysteinato(2-)]aquo-molybdate (V)} trihydrate
were prepared from aqueous solutions of molybdenum(VI) and cysteine following
published procedures28,34 . The Mo(VI) complex forms first, and is reduced to Mo(V)
complexes over time in aqueous solution with an excess of cysteine35.
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Mo binding to tannic acid and azotobactin. Mo complexation by tannic acid was
verified by titrating a 5.88 × 10-5 M solution of tannic acid in 10 mM ammonium acetate
(pH = 6.6) with a 1.11 × 10-3 M solution of sodium molybdate and monitoring the
ultraviolet-visible absorbance of the solution. The formation of Mo-azotobactin in the
presence of tannic acid was investigated by adding a solution of Mo and tannic acid to a
solution of azotobactin and monitoring the solution fluorescence at λ = 487 nm over time
(excitation wavelength λ = 380 nm).
XANES and EXAFS measurements and data processing
XAFS spectroscopy was used to provide information about the type, number, and radial
distances of the atoms surrounding Mo. Mo K-edge (20000 eV) XAFS spectroscopy
measurements were performed at beamline X18B at the NSLS (Brookhaven National
Laboratory) and at beamlines 11-2 and 4-3 at the SSRL (Menlo Park). However, the data
presented here were collected at NSLS. At beamline X18B (NSLS), a channel cut Si
(111) crystal was used as monochromator. The higher harmonics were rejected by
detuning the monochromator crystal by 30%. The incident ionization chamber was filled
with 100% N2 gas. The transmitted and reference ion chambers were filled with 100% Ar
gas. The fluorescence detector in the Stern-Heald geometry36 was also filled with Ar gas.
Mo foil was used as a reference and for energy calibration.
Solutions and homogeneous pallet samples were loaded into a slotted Plexiglas holder,
covered with Kapton film, and transported immediately to the beamline for XAFS
measurements. Prepared samples were kept refrigerated before XAFS measurements,
which were performed within 2-3 days of sample preparation.
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The data were analyzed using the methods described within the UWXAFS package37.
The background removal procedure is based on the AUTOBK method38 and implemented
by using the ATHENA interface to IFEFFIT39. The data sets were aligned and the
backgrounds were removed using ATHENA program. ATHENA was also used for
Linear Combination Fitting (LCF) of the unknown Mo samples to quantify the relative
contribution of different components in a given spectra. The fitting was done in the
normalized mu (E) space. Fitting range of -30 eV to +90 eV was used for proper
normalization of the XANES spectra. The input parameter to ATHENA that determines
the maximum frequency of the background, Rbkg, was set to 1.2 Å38. The data range used
for Fourier transforming the EXAFS χ(k) data was 3.0 – 10.5 Å-1 with a Hanning window
function and a delta k value of 1.0 Å-1 40. Simultaneous fitting with multiple k-weighting
(k1, k2, k3) was performed using the Fourier transformed χ(R) spectra. Fitting range was
1.2 – 4.0 Å. The simultaneous fitting approach reduces the possibility of obtaining
erroneous parameters due to correlations at any single k-weighting41
EXAFS data analysis is based on refining theoretical EXAFS spectra against the
experimental data. Models are constrained by use of crystalline model compounds with
well-characterized local structures. The crystallographic information of the standard
compounds were first transformed into a cluster of atoms by using the program
ATOMS42. Then FEFF843 was used to carry self-consistent quantum mechanical
calculations to simulate theoretical EXAFS spectra based on the cluster of atoms thus
obtained. Experimentally obtained EXAFS data on the standard compounds were fit to
these theoretically generated EXAFS spectra using the program FEFFIT39,40. We refined
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The data were analyzed using the methods described within the UWXAFS package37.
The background removal procedure is based on the AUTOBK method38 and implemented
by using the ATHENA interface to IFEFFIT39. The data sets were aligned and the
backgrounds were removed using ATHENA program. ATHENA was also used for
Linear Combination Fitting (LCF) of the unknown Mo samples to quantify the relative
contribution of different components in a given spectra. The fitting was done in the
normalized mu (E) space. Fitting range of -30 eV to +90 eV was used for proper
normalization of the XANES spectra. The input parameter to ATHENA that determines
the maximum frequency of the background, Rbkg, was set to 1.2 Å38. The data range used
for Fourier transforming the EXAFS χ(k) data was 3.0 – 10.5 Å-1 with a Hanning window
function and a delta k value of 1.0 Å-1 40. Simultaneous fitting with multiple k-weighting
(k1, k2, k3) was performed using the Fourier transformed χ(R) spectra. Fitting range was
1.2 – 4.0 Å. The simultaneous fitting approach reduces the possibility of obtaining
erroneous parameters due to correlations at any single k-weighting41
EXAFS data analysis is based on refining theoretical EXAFS spectra against the
experimental data. Models are constrained by use of crystalline model compounds with
well-characterized local structures. The crystallographic information of the standard
compounds were first transformed into a cluster of atoms by using the program
ATOMS42. Then FEFF843 was used to carry self-consistent quantum mechanical
calculations to simulate theoretical EXAFS spectra based on the cluster of atoms thus
obtained. Experimentally obtained EXAFS data on the standard compounds were fit to
these theoretically generated EXAFS spectra using the program FEFFIT39,40. We refined
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ab initio calculations on clusters of atoms derived from a known Mo-bis(catecholate)
crystal structure44 against the EXAFS data from Mo-azotochelin solution standards. The
best fit values of the path parameters obtained by independent modeling of the Mo-tannic
acid and Mo-LL samples at pH = 4.6, 6.1 and 7.5 were the same within uncertainties as
those obtained for the Mo-azotochelin standard. The sigma square (disorder factor) of the
Oax, Oeq, C and C-O and O-O signals (scattering paths) were thus set to be equal to the
ones obtained for the Mo-azotochelin standard reported in Table S2.
The value obtained for the EXAFS amplitude reduction factor for all standards was S02 =
0.9 ± 0.05 and this value was used in modelling the spectra from the unknown samples.
Statistically significantly lower R factor and 2νχ values were used as criteria for
improvement in the fit to justify the addition of an atomic shell to the model41.
XRF Mapping.
X-ray fluorescence (XRF) mapping was used to provide element specific information
about the spatial distribution of the atoms surrounding Mo. A Canberra 9-element Ge
Array detector was used for Mo XRF mapping at microscale using 5 x 5 micron beam.
Incident energy of X-ray was 21000 eV and a step size of 25 µm was used with 3 seconds
per pixel counting time. Soil samples were packed into a polycarbonate sample holder
and sealed with Kapton tape prior to transport to beamline X26A at the NSLS at
Brookhaven National Laboratory.
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2. Tables
Table S1. Chemical composition of soil and leaf litter layer samples collected in Arizona
and New Jersey (USA).
Metal carbon %
nitrogen %
Fe%
Moppm
AZ top-soil 32.3 1.01 2.1 23.8AZ sub-soil
(30 cm depth) 0.95 0.072 6.3 63.2
Pine Barrens leaf litter 52.2 0.82 0.06 5.2NJ top-soil 9.1 0.64 3.0 16.7NJ sub-soil
(50 cm depth) 0.77 0.095 4.6 35.9
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2. Tables
Table S1. Chemical composition of soil and leaf litter layer samples collected in Arizona
and New Jersey (USA).
Metal carbon %
nitrogen %
Fe%
Moppm
AZ top-soil 32.3 1.01 2.1 23.8AZ sub-soil
(30 cm depth) 0.95 0.072 6.3 63.2
Pine Barrens leaf litter 52.2 0.82 0.06 5.2NJ top-soil 9.1 0.64 3.0 16.7NJ sub-soil
(50 cm depth) 0.77 0.095 4.6 35.9
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Tables S2. Chemical structure parameters of Mo in complexes with leaf litter extract
(LL) and tannic acid
shell Distance (Å) coordination
number
Debye-Waller
Factor (x 10-3 Å2)
Mo-LL pH 6.1Mo-Oax 1.72 ± 0.01 2.04 ± 0.15 3.2*Mo-Oeq 1.99 ± 0.01 3.85 ± 0.36 8.0*Mo....C 2.93 ± 0.02 3.64 ± 0.62 4.0*Mo-S 2.45 ± 0.02 0.48 ± 0.10 5.8#
Mo....C-O 3.23 ± 0.03 4.0* 4.5*Mo....O-O 3.98 ± 0.03 4.0* 4.4*
Mo-azotochelin pH 6.1Mo-Oax 1.72 ± 0.01 2.14 ± 0.10 3.2 ± 0.8Mo-Oeq 2.01 ± 0.01 4.21 ± 0.35 8.0 ± 2.0Mo....C 2.95 ± 0.02 4.10 ± 0.40 4.0 ± 1.5
Mo....C-O 3.23 ± 0.03 4.0* 4.5 ± 1.5Mo....O-O 3.98 ± 0.03 4.0* 4.4 ± 1.2
Mo-LL pH 4.6 (¶)Mo-Oax 1.72 ± 0.01 2.04 ± 0.15 3.2*Mo-Oeq 1.99 ± 0.01 3.05 ± 0.32 8.0*Mo....C 2.93 ± 0.02 2.82 ± 0.32 4.0*Mo-S 2.45 ± 0.02 0.60 ± 0.12 5.8#
Mo....C-O 3.23 ± 0.03 4.0* 4.5*Mo....O-O 3.98 ± 0.03 4.0* 4.4*
Mo-LL pH 7.5Mo-Oax 1.72 ± 0.01 2.04 ± 0.15 3.2*Mo-Oeq 1.99 ± 0.01 3.85 ± 0.46 8.0*Mo....C 2.93 ± 0.02 3.14 ± 0.55 4.0*Mo-S 2.45 ± 0.02 0.67 ± 0.16 5.8#
Mo....C-O 3.23 ± 0.03 4.0* 4.5*Mo....O-O 3.98 ± 0.03 4.0* 4.4*
Mo-Tannic AcidMo-Oax 1.73 ± 0.01 2.24 ± 0.15 3.2*Mo-Oeq 2.05 ± 0.01 3.46 ± 0.38 8.0*Mo....C 2.94 ± 0.02 3.04 ± 0.42 4.0*
Mo....C-O 3.25 ± 0.03 4.0* 4.5*Mo....O-O 3.97 ± 0.03 4.0* 4.4*
¶Mo(VI) polymerization in the sample was ruled out by the lack of Mo-Mo peak in the EXAFS Fourier transform spectrum45.* set to the best fit value of the azotochelin standard# set to the best fit value of the Mo-cysteine standard
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Figure S1 Linear Combination Fitting (LCF) of Mo K-edge XANES spectra of soil samples.
a, and b, Mo-spiked soil samples (hardwood forest, NJ, USA). c, Mo-spiked leaf litter extract
(Mo-LL, Pine Barrens, NJ, USA).
20000 20020 20040 20060 20080 20100
0.0
0.3
0.6
0.9
1.2a
Norm
alize
d Ab
sorb
ance
µ(E)
x Top-soil
Mo-top soil, pH 5.7 LCF Mo-geothite, pH 5.4 Mo-LL, 5.3 residue
E (eV)
20000 20020 20040 20060 20080 20100
0.0
0.3
0.6
0.9
1.2b
Norm
alize
d Ab
sorb
ance
µ(E)
x Sub-soil
Mo-top soil, pH 5.7 LCF
Mo-ferrihydrite, pH 4.4 Mo-geothite, pH 5.4 Mo-LL, pH 5.3 residue
E (eV)
20000 20020 20040 20060 20080 20100
0.0
0.3
0.6
0.9
1.2
c
Norm
alize
d Ab
sorb
ance
µ(E)
x Leaf leachates
Mo-LL, pH 6.1 LCF Mo-azotochelin, pH 6.1 Mo-cysteine, crystaline Residue
E (eV)
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Figure S1 Linear Combination Fitting (LCF) of Mo K-edge XANES spectra of soil samples.
a, and b, Mo-spiked soil samples (hardwood forest, NJ, USA). c, Mo-spiked leaf litter extract
(Mo-LL, Pine Barrens, NJ, USA).
20000 20020 20040 20060 20080 20100
0.0
0.3
0.6
0.9
1.2a
Norm
alize
d Ab
sorb
ance
µ(E)
x Top-soil
Mo-top soil, pH 5.7 LCF Mo-geothite, pH 5.4 Mo-LL, 5.3 residue
E (eV)
20000 20020 20040 20060 20080 20100
0.0
0.3
0.6
0.9
1.2b
Norm
alize
d Ab
sorb
ance
µ(E)
x Sub-soil
Mo-top soil, pH 5.7 LCF
Mo-ferrihydrite, pH 4.4 Mo-geothite, pH 5.4 Mo-LL, pH 5.3 residue
E (eV)
20000 20020 20040 20060 20080 20100
0.0
0.3
0.6
0.9
1.2
c
Norm
alize
d Ab
sorb
ance
µ(E)
x Leaf leachates
Mo-LL, pH 6.1 LCF Mo-azotochelin, pH 6.1 Mo-cysteine, crystaline Residue
E (eV)
11
Figure S2. Linear Combination Fitting of the XANES spectrum of the Mo-spiked leaf
litter extract (Mo-LL, Pine Barrens, NJ, USA) at pH = 9.
20000 20020 20040 20060 20080 20100
0.0
0.3
0.6
0.9
1.2 Leaf LeachatespH 9.0
Norm
alize
d Ab
sorb
ance
µ(E)
x
Mo-LL, pH 9.0 LCF
Mo-azotochelin, pH 6.1 Molybdate, pH 5.8 residue
E (eV)
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Figure S3. Ultraviolet-visible difference spectra of Mo-LL (black) and Mo-tannic acid
(blue) at pH 6.6. The difference spectrum of Mo-LL is obtained by subtracting the
spectrum of the leaf litter extract (LL) from that of the Mo-LL solution, prepared by
adding 1.0 mM molybdate to (LL). The difference spectrum of Mo-tannic acid is
obtained in a similar fashion by subtracting the spectrum of tannic acid from that of the
Mo-tannic acid solution. The spectrum of the 1:1 Mo-azotochelin complex at pH 6.6 (red)
is shown for comparison.
300 400 500 6000.0
0.1
0.2
0.3
0.4
0.5
0.6
Abso
rban
ce (U
)
Wavelength (nm)
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Figure S3. Ultraviolet-visible difference spectra of Mo-LL (black) and Mo-tannic acid
(blue) at pH 6.6. The difference spectrum of Mo-LL is obtained by subtracting the
spectrum of the leaf litter extract (LL) from that of the Mo-LL solution, prepared by
adding 1.0 mM molybdate to (LL). The difference spectrum of Mo-tannic acid is
obtained in a similar fashion by subtracting the spectrum of tannic acid from that of the
Mo-tannic acid solution. The spectrum of the 1:1 Mo-azotochelin complex at pH 6.6 (red)
is shown for comparison.
300 400 500 6000.0
0.1
0.2
0.3
0.4
0.5
0.6
Abso
rban
ce (U
)
Wavelength (nm)
13
Figure S4. k2 Weighed χ(k) data (black lines) and fit (red circles) for Mo K-edge EXAFS
of Mo-LL and Mo-azotochelin at different pH values.
4 6 8 10-1
0
1
2
3
4
Mo-LL (pH 7.5)
Mo-Azotochelin (pH 6.1)
Mo-LL (pH 6.1)
Mo-LL (pH 4.6)
k2 * χ(
k) (Å
-3)
k (Å-1)
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4. Acknowledgments
Total nitrogen and carbon content analysis were performed by Jim Wang from the LSU
AgCenter, Baton Rouge, LA. µXRF and µXANES were performed at Beamline X26A,
National Synchrotron Light Source (NSLS), Brookhaven National Laboratory. X26A is
supported by the Department of Energy (DOE) - Geosciences (DE-FG02-92ER14244 to
The University of Chicago - CARS) and DOE - Office of Biological and Environmental
Research, Environmental Remediation Sciences Div. (DE-FC09-96-SR18546 to the
University of Kentucky). Use of the NSLS was supported by DOE under Contract No.
DE-AC02-98CH10886.
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4. Acknowledgments
Total nitrogen and carbon content analysis were performed by Jim Wang from the LSU
AgCenter, Baton Rouge, LA. µXRF and µXANES were performed at Beamline X26A,
National Synchrotron Light Source (NSLS), Brookhaven National Laboratory. X26A is
supported by the Department of Energy (DOE) - Geosciences (DE-FG02-92ER14244 to
The University of Chicago - CARS) and DOE - Office of Biological and Environmental
Research, Environmental Remediation Sciences Div. (DE-FC09-96-SR18546 to the
University of Kentucky). Use of the NSLS was supported by DOE under Contract No.
DE-AC02-98CH10886.
15
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38 Newville, M., Livins, P., Yacoby, Y., Rehr, J. J. & Stern, E. A. Near edge X-ray
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