s1 measurements of fe(ii) and total fe … · web view2state key laboratory of biogeology and...
TRANSCRIPT
Supporting Information
Electron Transfer Between Sorbed Fe(II) and Structural Fe(III) in Smectites and its Effects
on Nitrate-Dependent Iron Oxidation by Pseudogulbenkiania sp. strain 2002
Li Zhang1, Hailiang Dong1,2*, Ravi K. Kukkadapu3*, Qusheng Jin4, and Libor Kovarik3
1Department of Geology and Environmental Earth Science
Miami University, Oxford, OH 45056, USA
2State Key Laboratory of Biogeology and Environmental Geology
China University of Geosciences, Beijing 100083, China
3EMSL, Pacific Northwest National Laboratory, Richland, WA 99352, USA
4Department of Earth Sciences, University of Oregon, Eugene, OR 97403
*Corresponding authors: Hailiang Dong
Tel: 513 529 2517; Fax: 513 529 1542; Email: [email protected]
Ravi Kukkadapu: 509-371-6384; Email: [email protected]
Revised for Geochimica et Cosmochimica Acta
August 10, 2019
S1
1
2
3
4
5
6
7
8
910
11
12
13
14
15
16
17
18
19
20
S1 Measurements of Fe(II) and total Fe concentrations
To prevent any underestimation of Fe(II) concentration due to its rapid reaction with
nitrite under acidic conditions that is required for a typical Fe(II) assay (Zhao et al., 2013), nitrite
was separated from Fe(II)-bearing clay minerals by three washes with sterile and anoxic buffers
followed by centrifugation at 10,000 × g for 10 min. (Zhao et al., 2017). Fe(II) concentration was
measured colorimetrically with 1,10 phenanthroline (Amonette and Templeton, 1998) after clay
digestion with a combination of HF and H2SO4. Total Fe concentration was determined by first
reducing Fe(III) to Fe(II) with hydroxylamine hydrochloride and subsequently measured with the
same method. Fe(III) concentration was determined by the difference between total Fe and
Fe(II). To monitor any Fe(II) desorption from clay surface, time course change of aqueous Fe2+
concentration was measured on the supernatant following centrifugation (10,000 × g for 10 min).
The result showed that there was essentially no Fe(II) desorption under the conditions used in
this study.
S2 Biogeochemical Reaction Modeling
Model validation and sensitivity analysis
We validate the model of microbial iron oxidation using independent laboratory
observations – the observations that have not been applied in our model development.
Specifically, Weber and colleagues monitored the metabolism of strain 2002 in a medium
containing Fe2+ and nitrate (Weber et al., 2001). We apply the model by using the chemical
conditions of their experiments, and simulate the progress of Fe2+ oxidation, nitrate reduction,
and the growth of strain 2002. As shown in Fig. S5, by using a rate constant kFe of 5.0±0.7×106
S2
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
kg·gcdw-1·s1, the model describes well the progress of Fe2+, nitrate consumption and the growth of
strain 2002 observed in the laboratory experiments.
We also analyze the sensitivity of the model to microbial parameters. Following the
framework of metabolic control analysis (Fell, 1992), we calculate the sensitivity of microbial
iron reduction rate r to model parameter p according to
We compute the sensitivity by simulating the growth of strain 2002 in batch reactors that contain
3 mM Fe(II) and 6 mM nitrate at pH 6, the same conditions used in our experiments. According
to the modeling results, the rate is most sensitive to the rate constant kFe (a sensitivity of
0.94), but relatively insensitive to the growth yield Y, the specific maintenance rate D, or the
half-saturation constant KA for nitrate (a sensitivity of 0.01, 0.001, and 0, respectively).
Based on these results, we conclude that the progress of microbial iron oxidation observed in our
experiments can be applied to estimate the rate constant kFe of microbial iron oxidation.
Thermodynamic database
We added into the thermodynamic dataset the entries for ferrous iron sorbed onto the two
different sites, the basal plane and the edge site, of nontronite and montmorillonite, and saved the
dataset as thermo.com.V8.R6+.S2002.tdat. Specifically, the entry for ferrous iron sorbed on the
basal plan of montmorillonite is:
Montmor-6B type= Smectite formula= Fe.107Na.33Mg.33Al1.67Si4O10(OH)2.214 mole vol.= 0.0000 cc mole wt.= 376.6322 g 7 species in reaction -6.214 H+ .330 Mg++ .330 Na+
S3
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
6061626364
1.670 Al+++ 4.214 H2O 4.000 SiO2(aq) .107 Fe++ 3.5459 2.4844 .4327 -1.7940 -4.1631 -6.1636 -7.9650 -9.7369
The entry for ferrous iron sorbed on the edge site is:
Montmor-8E type= Smectite formula= Fe.319Na.33Mg.33Al1.67Si4O10(OH)2.638 mole vol.= 0.0000 cc mole wt.= 395.6828 g 7 species in reaction -6.638 H+ .330 Mg++ .330 Na+ 1.670 Al+++ 4.638 H2O 4.000 SiO2(aq) .319 Fe++ 3.5459 2.4844 .4327 -1.7940 -4.1631 -6.1636 -7.9650 -9.7369
The entry for ferrous iron sorbed on the basal plan of nontronite is:
Nontronite-6B type= Smectite formula= Ca.165Fe2.152Al.33Si3.67H2.304O12.304 mole vol.= 131.1000 cc mole wt.= 437.9521 g 7 species in reaction -7.624 H+ .165 Ca++ .330 Al+++ 2.000 Fe+++ 3.670 SiO2(aq) 4.964 H2O 0.152 Fe++ -11.3915 -11.5822 -12.6234 -13.9486 -15.4751 -16.8671 -18.2346 -19.7093
The entry for ferrous iron sorbed on the edge site is:
Nontronite-8E type= Smectite formula= Ca.165Fe2.267Al.33Si3.67H2.534O12.534 mole vol.= 131.1000 cc mole wt.= 448.2861 g 7 species in reaction -7.854 H+ .165 Ca++ .330 Al+++ 2.000 Fe+++ 3.670 SiO2(aq) 5.194 H2O 0.267 Fe++ -11.3915 -11.5822 -12.6234 -13.9486 -15.4751 -16.8671 -18.2346 -19.7093
Input Scripts
The input script for simulating microbial oxidation of dissolved ferrous and reduction of
nitrate to nitrogen gas (N2) at pH 6:
data = thermo.com.V8.R6+.S2002.tdat
S4
6566676869
707172737475767778
79
808182838485868788
89
90919293949596979899
100
101
102
time start = 0 day, end = 6 daytemperature = 25 Cdecouple ALLH2O = 1 free kgNa+ = 50 mmol/kgCl- = 50 mmol/kgbalance on Cl-Fe++ = 3 mmol/kgswap Goethite for Fe+++Goethite = .1 free mmol/kgNO3- = 6.14 mmol/kgNO2- = .01 mmol/kgpH = 6swap Acetate for Acetic_acid(aq)Acetate = .5 mmol/kgN2(aq) = .001 mmol/kgHCO3- = 1 mmol/kgkinetic microbe-1 rxn = "Fe++ + 1.5 H2O + .5 NO3- -> Goethite + 2 H+ + .5 NO2-" biomass = 100 rate_law = file "FeOx.bas" rate_con = 1.5e-8 KD = 2.0e-3 KA = 2.3e-6 mpower(NO3-) = 1 mpowerA(NO3-) = 1 growth_yield = 200 decay_con =1e-7
kinetic microbe-2 rxn = "Acetate + .6 H+ + 1.6 NO3- -> 2 HCO3- + .8 N2(aq) + .8 H2O" biomass = 50 rate_con = 1e-9 KA = 2.3e-6 mpower(NO3-) = 1 mpowerA(NO3-) = 1 ATP_energy = 1 ATP_number = -45 growth_yield = 11000 decay_con = 1e-7fix pHprecip = off
The rate law file "FeOx.bas":Fe_II = totmolal("Fe++")Threshold = KDFK = Fe_II*molality("NO3-")/(molality("NO3-")+KA)rate = Wmass*rate_con*biomass*FK*(1-QoverK)IF (Fe_II < Threshold) THEN rate = 0rprime0 = dndt0/(biomass0 * Wmass)rpave = (1.0-Theta)*rprime0 + Theta*rprimebiom = biomass0*exp((growth_yield*rpave-decay_con)*Deltat)IF biom < 0.0 THEN biom = 0.0setgwbvar("biomass", biom)end_block:return rprime * biomass * Wmass
Note that we use KD in the input file represents the threshold of ferrous iron oxidation. To
simulate the experiments at pH 8, we set pH at 8 and KD at 4.0e-4.
S5
103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144
145
To simulate microbial oxidation of ferrous iron sorbed onto the basal plan of
montmorillonite, we swapped Montmor-6B for aqueous ferrous iron and added the
corresponding aqueous components for the mineral:
pH = 6swap Montmor-6B for Fe++Montmor-6B = 28 free mmol/kgMg++ = .05 mmol/kgAl+++ = .05 mmol/kgSiO2(aq) = .05 mmol/kgprecip off
We also replace the entry for microbial reaction:
kinetic microbe-1 rxn = "Montmor-6B + .0535 NO3- -> .0535 H2O + Montmor-Na\ + .107 Goethite + .0535 NO2-"\ rate_law = file "Montmor-6B_OX.bas" biomass = 100 rate_con = 2.1e-8 KA = 2.3e-6\ KD = 2.03e-2 mpower(NO3-) = 1 mpowerA(NO3-) = 1 growth_yield = 39.4\ decay_con =1e-7
The rate law "Montmor-6B_OX.bas" contains the following entries:Fe_II = mass("Montmor-6B")*0.107Threshold = KD*0.107FK = Fe_II*molality("NO3-")/(molality("NO3-")+KA)rate = Wmass*rate_con*biomass*FK*(1-QoverK)IF (Fe_II < Threshold) THEN rate = 0rprime0 = dndt0/(biomass0 * Wmass)rpave = (1.0-Theta)*rprime0 + Theta*rprimebiom = biomass0*exp((growth_yield*rpave-decay_con)*Deltat)IF biom < 0.0 THEN biom = 0.0setgwbvar("biomass", biom)end_block:return rprime * biomass * Wmass
Note that the 0.107 mol ferrous iron is sobred onto the basal plane of 1 mol of montmorillonite
(see Table S1).
Likewise, we used the following entries to simulate microbial oxidation of ferrous iron
sorbed on the edge sites of montmorillonite:
pH = 8swap Montmor-8E for Fe++
S6
146
147
148
149150151152153154155
156
157158159160161
162163164165166167168169170171172173174
175
176
177
178
179180181
Montmor-8E = 9.5 free mmol/kgMg++ = .05 mmol/kgAl+++ = .05 mmol/kgSiO2(aq) = .05 mmol/kgprecip off
The entry for microbial reaction is
kinetic microbe-1 rxn = "Montmor-8E + .1595 NO3- -> .1595 H2O + Montmor-Na + .319 Goethite + .1595 NO2-" biomass = 100 rate_law = file "Montmor-8E_OX.bas.bas" rate_con = 3.1e-8 KA = 1e-5 KD = 2.0e-3 mpower(NO3-) = 1 mpowerA(NO3-) = 1 growth_yield = 63.8 decay_con = 1e-7
The rate law "Montmor-8E_OX.bas" contains the following entries:
Fe_II = mass("Montmor-8E")*0.319Threshold = KD*0.319FK = Fe_II*molality("NO3-")/(molality("NO3-")+KA)rate = Wmass*rate_con*biomass*FK*(1-QoverK)IF (Fe_II < Threshold) THEN rate = 0rprime0 = dndt0/(biomass0 * Wmass)rpave = (1.0-Theta)*rprime0 + Theta*rprimebiom = biomass0*exp((growth_yield*rpave-decay_con)*Deltat)IF biom < 0.0 THEN biom = 0.0setgwbvar("biomass", biom)end_block:return rprime * biomass * Wmass
To simulate microbial oxidation of ferrous iron sorbed onto the basal plan of nontronite,
we used the following entries:
pH = 6swap Nontronite-6B for Fe++Nontronite-6B = 21 free mmol/kgMg++ = .05 mmol/kgAl+++ = .05 mmol/kgSiO2(aq) = .05 mmol/kgkinetic microbe-1 rxn = " Nontronite-6B + .076 NO3- -> .076 H2O + \ Nontronite-Ca + .152 Goethite + .076 NO2-" \ rate_law = file "Nontronite-6B_OX.bas" biomass = 100 rate_con = 1.1e-8\ KA = 2.3e-6 KD = 9.92e-2 mpower(NO3-)=1 mpowerA(NO3-) = 1\ growth_yield = 30.4 decay_con = 1e-7
The rate law "Nontronite-6B_OX.bas" contains the following entries:Fe_II = mass("Nontronite-6B")
S7
182183184185186187188
189190191192193194195196197198199200201202203204205206207208209
210
211212213214215216217218219220221222223224
Threshold = KD*0.152FK = Fe_II*molality("NO3-")/(molality("NO3-")+KA)rate = Wmass*rate_con*biomass*FK*(1-QoverK)IF (Fe_II < Threshold) THEN rate = 0rprime0 = dndt0/(biomass0 * Wmass)rpave = (1.0-Theta)*rprime0 + Theta*rprimebiom = biomass0*exp((growth_yield*rpave-decay_con)*Deltat)IF biom < 0.0 THEN biom = 0.0setgwbvar("biomass", biom)end_block:return rprime * biomass * Wmass
To simulate microbial oxidation of ferrous iron sorbed onto the edge sites of nontronite,
we used the following entries:
pH = 8swap Nontronite-8E for Fe++Nontronite-8E = 11.25 free mmol/kgMg++ = .05 mmol/kgAl+++ = .05 mmol/kgSiO2(aq) = .05 mmol/kgprecip offkinetic microbe-1 rxn = " Nontronite-8E + .1335 NO3- -> .1335 H2O + \ Nontronite-Ca + .267 Goethite + .1335 NO2-" \ rate_law = file "Nontronite-8E_OX.bas" biomass = 100 rate_con = 3.0e-8 \ KA = 2.3e-6 KD = 1.38e-2 mpower(NO3-)=1 mpowerA(NO3-) = 1\ growth_yield = 53.4 decay_con = 1e-7
The rate law "Nontronite-8E_OX.bas" contains the following entries:Fe_II = mass("Nontronite-8E")Threshold = KD*0.267FK = Fe_II*molality("NO3-")/(molality("NO3-")+KA)rate = Wmass*rate_con*biomass*FK*(1-QoverK)IF (Fe_II < Threshold) THEN rate = 0rprime0 = dndt0/(biomass0 * Wmass)rpave = (1.0-Theta)*rprime0 + Theta*rprimebiom = biomass0*exp((growth_yield*rpave-decay_con)*Deltat)IF biom < 0.0 THEN biom = 0.0setgwbvar("biomass", biom)end_block:return rprime * biomass * Wmass
S8
225226227228229230231232233234235236237
238
239240241242243244245246247248249250251252253254255256257258259260261262263264
S3 Electron balance calculation
In order to determine the extent of interfacial electron transfer (IET) and help identify
various Fe(II) species as a result of IET, electron balance calculations were carried out using
published data.(Schaefer et al., 2011; Latta et al., 2017) The basic principle is that upon sorption
of Fe(II) to clay minerals, there is electron transfer between sorbed Fe(II) and structural Fe(III).
These two previous studies performed sorption of Mössbauer-invisible 56Fe(II) to NAu-2 at pH
7.5(Schaefer et al., 2011) and to montmorillonite at pH 4-7.5(Latta et al., 2017). The extent of
reduction of structural Fe(III) (of natural isotopic abundance) in these clay minerals was
monitored over time and a stoichiometric ratio between the amount of sorbed Fe(II) oxidation
and the amount of structural Fe(III) reduction was established. Although it was not explicitly
stated, this electron transfer process should be driven by a gradient in electron density. In other
words, if the clay minerals are fully reduced, there should not be any IET. When the NAu-2 or
SWy-2 structure has a certain amount of initial structural Fe(II), the amount of IET should be
proportionally decreased. No published data are available to perform electron balance calculation
for NAu-2 at pH 6. In the following paragraphs, we describe electron balance calculation for the
other three cases (NAu-2 pH 8, SWy-2 pH 6 & 8).
Schaefer et al. reported that at a similar pH (7.5) reduction of structural Fe(III) in NAu-2
by sorbed Fe(II) is a 1:1 stoichiometric ratio when sorbed Fe(II)/Total Fe in clay is < 15%.
(Schaefer et al., 2011) Our sorbed Fe(II)/total Fe ratio in NAu-2 is 12.6% (e.g.,
(3.51-0.583)%/(0.583+22.6)%, Table 1, here total Fe in NAu-2 is before sorption), thus, after
IET, the Fe(II)/total Fe ratio in the NAu-2 structure should be ~12.6% (or 2.93% Fe(II) by clay
weight or 2.93/(3.51+22.0) = 11.5% by Fe(II)/total Fe ratio, Table S3, here total Fe in NAu-2 is
after sorption to make it comparable to Mössbauer-fitted ratio). Considering that an initial Fe(II)
S9
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
present in the pristine NAu-2 (0.583% by weight), 2.35% structural Fe(II) (or 9.21% Fe(II)/total
Fe ratio) should be newly produced, and the other 0.580% (or 2.27% Fe(II)/total Fe ratio) should
remain sorbed. Thus the structural Fe(II)/total Fe ratio in the NAu-2 structure (11.5%) is fairly
consistent with our Mössbauer fitted ratio of 9.8% for structural Fe(II) (Table S2). Residual
sorbed Fe(II) (2.27%) should be associated with newly generated goethite and magnetite.
For SWy-2 at pH 6, the ratio of sorbed Fe(II)/total Fe in SWy-2 is
(1.63-0.202)/(0.202+2.88) = 46.4%, which, according to the stoichiometric reaction between
sorbed Fe(II) and structural Fe(III) in SWy-2(Latta et al., 2017) should produce ~46.4%
Fe(II)/total Fe in the SWy-2 structure (or 1.43 % Fe(II) by clay weight). Considering there is
0.202% initial Fe(II) in the original SWy-2 (Table 1), 1.23% structural Fe(II) should be newly
generated through reduction of structural Fe(III) by sorbed Fe(II) through IET. Therefore, 1.23%
sorbed Fe(II) should have been consumed to reduce structural Fe(III), which, together with the
initial amount of Fe(II) in the SWy-2 structure (0.202% wt.), should produce ~32.1% Fe(II) [e.g.,
1.43/(1.63+2.83) = 32.1% Fe(II)/total Fe ratio], which is close to our Mössbauer fitted value of
38.4% (150 K) or 41.7% (12 K). Correspondingly the amount of sextet production should be
~32.1%, however, for this sample, the pristine SWy-2 also has some sextet to begin with,
therefore the Mössbauer fitted value of sextet area is greater than 32.1%. A small fraction of
original sorbed-Fe(II) is not oxidized and should remain sorbed (onto goethite or the
nanoparticles).
For SWy-2 at pH 8, using the same method, we estimate that approximately 70%
structural Fe(II) can be achieved from 151% sorbed Fe/total Fe ratio (e.g.,
(4.86-0.202)/(0.202+2.88) = 151%), which amounts to 2.16% structural Fe(II) by weight or
28.4% in terms of Fe(II)/total Fe ratio (Table S3). Therefore, the amount of sorbed Fe(II) that is
S10
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
not oxidized should be 4.86-2.16 = 2.70% by weight or 35.5% in terms of Fe(II)/total Fe ratio).
Considering there is an initial amount of Fe(II) in SWy-2 (0.202 %), the amount of new sextet
formation from the oxidation of a fraction of sorbed Fe(II) should be 2.16-0.202 = 1.96% (or
1.96/7.61 = 25.8% in terms of Fe(II)/total Fe ratio), which is higher than the Mossbauer-derived
fitting value of 16.8% (Table S2), suggesting that some newly formed Fe(III) may not be present
in sextet, but instead as a doublet. The residual amount of Fe(II) (2.70% by weight or 35.5% in
terms of Fe(II)/total Fe ratio) occurs as the inner doublet (the mixed Fe(II)-Fe(III) nanoparticles)
and is magnetically ordered at 12 K (Table S2).
In summary, 80.2% of the Fe(II) sorbed to NAu-2 at pH 8 (2.35/2.93 = 80.2% in Table
S3) is oxidized to goethite and a mixed-valence magnetite phase. However, the trend of
oxidation of sorbed-Fe(II) is opposite for SWy-2: 86.0% (1.23/1.43 = 86.0%) of the Fe(II)
sorbed to SWy-2 is oxidized to goethite and nanoparticles at pH 6, but only 42% (1.96/4.66 =
42.1%) at pH 8 is to oxidized goethite and the remaining Fe(II) occurred as highly reactive
Fe(II)-Fe(III) nanoparticles (either sorbed or structural).
S11
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
Table S1 Summary of studies on Fe2+ sorption capacity onto various clay minerals
Clay Mineral pH Method to measure Fe2+
Fe2+ Sorption capacity (mmol/g)
Reference
NAu-2 6.0 1,10-phen 0.25 This study8.0 0.52
SWy-2 6.0 0.268.0 0.84
NAu-2 6.0 Ferrozine ~0.22 (Jaisi et al., 2008)(Jaisi et al., 2008)
8.0 ~0.22
SYn-1 (0% wt. Fe(III)) 4.0 0.0477 (Neumann et al., 2013)(Neumann et al., 2013)
7.5 0.312NAu-1 4.0 0.241
6.0 0.2826.5 0.3277.5 0.920
NAu-1 6.0 1,10-phen 0.364 (calculated average from time course)
(Neumann et al., 2015)(Neumann et al., 2015)
7.5 0.907NAu-2 6.0 0.637
7.5 0.955SWa-1 (15.4% wt. Fe(III))
6.9 0.0222
MAu-1(2.1% wt. Fe(III)) 6 ICP-OES ~0.15 (Tsarev et al., 2016)(Tsarev et al., 2016)
8 ~1NAu-1(25.2% wt. Fe(III)) 6 ~0.15
8 ~1NAu-2 (26.5% wt. Fe(III))
6 ~0.15
8 ~1
SWy-2 4.0 1,10-phen 0.142 (Latta et al., 2017)(Latta et al., 2017)
6.0 0.3637.0 0.5847.5 0.954
S12
326
Table S2 Mössbauer spectrum parameters
Sample Temp Site CS1 QS2 σQS3 ε4 HFD5 σHFD
6 %7 χ2 8 Chemical9
(t final) (mm/sec)
(mm/sec)
(mm/sec)
(mm/sec)
(Tesla) (Tesla) (%)
NAu-2 12 K Fe(III)-1 0.48 0.35 0.3 __ __ __ 65.9 0.83 97.4Fe(III)-1' 0.53 1.24 0.06 __ __ __ 29.3Fe(III)-tet 0.42 0.5 0.09 __ __ __ 5.1
NAu-2 Fe(II) 12 K Fe(II)-1 1.25 2.68 0.125 __ __ __ 8.6 0.98 8.2pH6 Fe(III)-1 0.51 0.36 0.19 __ __ __ 68.5 91.8
Fe(III)-1' 0.59 1.03 0.35 __ __ __ 28.5
NAu-2 Fe(II) 12 K Fe(II)-1 1.27 2.68 0.07 __ __ __ 8.5 1.3 6.6bacteria Fe(III)-1 0.5 0.33 0.17 __ __ __ 65.5pH6 Fe(III)-1' 0.48 1.03 0.17 __ __ __ 20.8 93.4
lepidocrocite 0.39 __ __ 0.18 43.9 3 5.2
NAu-2 Fe(II) 12 K Fe(II)Fe(III)
1.22 2.86 0.1 __ __ __ 9.8 0.95 13.8pH8 0.47 0.46 0.29 __ __ __ 55.2 86.2
Ferrihydrite-like Fe
oxides 0.48 __ __ -0.11 39.31 21.3 35.0
NAu-2 Fe(II) 12 K Fe(II)-1 1.22 2.8 0.0008 __ __ __ 5.4 0.96 4.6bacteria Fe(III)-1 0.48 0.47 0.3 __ __ __ 57.5 95.4pH8 Ferrihydrite-like Fe
oxides 0.51 __ __ -0.14 40.5 21.7 37.1
SWy-2 Fe(II) 150 K Fe(II)-1 1.27 3.03 0.18 __ __ __ 38.4 0.82 36.6pH6 Fe(III) 0.32 0.33 0.18 __ __ __ 18.5 63.4
Goethite + clay-Fe(III) 0.52 __ __ -0.05 44.7 3.08 43.4
S13
327
12 K Fe(II)-1 1.28 3.05 0.11 __ __ __ 41.7 0.93 36.6Fe(III) 0.35 0.43 0.26 __ __ __ 14.9 63.4Goethite + clay-Fe(III) 0.48 __ __ -0.11 49.5 0.75 43.4
SWy-2 Fe(II) 150 K Fe(II)-1 1.25 3.05 0.18 __ __ __ 26.2 1.7 25.8bacteria Fe(III) 0.48 0.71 0.31 __ __ __ 44.6 74.2pH6 Goethite + clay-Fe(III) 0.49 __ __ -0.07 43.2 6.92 29.2
12 K Fe(II)-1 1.28 3.08 0.13 __ __ __ 24.2 1.8 25.8Fe(III) 0.49 0.69 0.39 __ __ __ 22.7 74.2Goethite + clay-Fe(III)-1 0.5 __ __ -0.09 49 1.5 24.3Goethite + clay-Fe(III)-2 0.42 __ __ 0.02 47.4 7.1 28.8
SWy-2 Fe(II) 150 K Fe(II)-1 1.27 2.85 0.22 __ __ __ 38.9 0.8 63.9pH8 Fe(II)-2 1.35 2.07 0.12 __ __ __ 33
Fe(III) 0.55 0.55 0.41 __ __ __ 14.4 36.1Goethite + clay-Fe(III) -0.09 __ __ -0.09 45.7 3 13.7
__ __ __12 K Fe(II)-1 1.29 2.83 0.1 42.2 0.85 63.9
Fe(II)-2-magnetic 1.35 __ __ 1.04 18.1 0.01 28Fe(III) 0.44 0.6 0.2 __ __ __ 13 36.1Goethite + clay-Fe(III) 0.41 __ __ 0.007 49.2 2 16.8
SWy-2 Fe(II) 150 K Fe(II)-1 1.22 2.96 0.3 __ __ __ 10.1 1.2 13.3bacteria Fe(III) 0.49 0.59 0.29 __ __ __ 35.5 86.7pH8 Goethite + clay-Fe(III) 0.46 __ __ 0.14 46.3 2.3 54.4
12 K Fe(II) -1 1.33 3.1 0.3 __ __ __ 11.1 0.9 13.3Fe(III) 0.52 0.58 0.29 __ __ __ 30.1 86.7Goethite + clay-Fe(III) 0.48 __ __ -0.12 49.6 1.3 58.2
1center shift; 2quadrupole splitting (QS); 3QS standard deviation;4 quadrupole splitting parameter; 5magnetic hyperfine field (HFD);6HFD standard deviation; 7relative contribution (assuming identical recoilless fractions for all the species);8goodness of fit; 9Chemical method can only determine total Fe(II) and Fe(III) contents, not contents of individual Fe species.
S14
328329330331
Table S3 Summary of electron balance calculations following Fe2+ sorption
Clay pH [Fe(II)initially sorbed]
(wt.% in clay or
mmol/g)
[Fe(II)Initially sorbed]/Total Fein clay1
(%)
[Structural Fe(II)]/Total Fe
in clay after IET2
(%)
Structural Fe(II) after IET
Initial clay structural
Fe(II) 7
(wt.% in clay or
mmol/g)
Newly produced clay structural Fe(II)
from IET
Residual fraction of the sorbed Fe(II)
after IET
5(wt.% in clay or mmol/g)
6(% of total Fe)
8(wt.% in clay or mmol/g)
9(% in total Fe)
10(wt.% in clay or mmol/g)
11(% in total Fe)
NAu-2 8.0 2.93 (0.525)
12.6 ~12.63 2.93 (0.525)
11.5 0.583 (0.104)
2.35 (0.421)
9.23 0.580 (0.104)
2.27
SWy-2 6.0 1.43 (0.256)
46.4 ~46.44 1.43 (0.256)
32.1 0.202 (0.036)
1.23 (0.220)
27.6 0.200 (0.036)
4.48
8.0 4.66
(0.835)
151 ~704 2.16
(0.387)
28.4 0.202
(0.036)
1.96
(0.351)
25.8 2.70
(0.484)
35.5
Fe(II) in clay is expressed in both wt% and mmol/g (in parenthesis). Fe(II) relative to total Fe is in % only. 1Calculted using data in Table 1 as sorbed Fe(II) divided by total Fe in pre-sorption clay;2 This column of data is obtained based on references on stoichiometric electron transfer between sorbed Fe(II) and structural Fe(III).3 based on data in Schaefer et al., for pH 7.5 (their Fig. 4)(Schaefer et al., 2011); 4Latta et al. (their Fig. 8)(Latta et al., 2017); 5Calculated by multiplying [structural Fe(II)]/Total Fe in clay (column 5) by Total Fe in pre-sorption clay (Table 1, last column); 6Calculated by dividing structural Fe(II) by total Fe in clay (with Fe2+ sorption); 7Initial Fe(II) in each clay (Table 1); 8Calculated by the difference between the total Fe(II) and initial amount of Fe(II); 9Calculated by dividing Fe(II)8 by total Fe in clay (with Fe2+ sorption); 10Calculated by the difference between the total amount of sorbed Fe(II) and the amount used to reduce structural Fe(III)8; 11Calculated by dividing Fe(II)10 by total Fe in clay (with Fe2+ sorption).
S15
332
333
334335336337338339340
Fig. S1. Nitrate reduction during the growth of strain 2002 in the presence of either acetate or
aqueous Fe2+ (10 mM) as electron donor.
S16
341
342
343
344
Fig. S2. Nitrate reduction by strain 2002 cells at pH 6 & 8. Electron donor is inferred to be from
stored carbon within cells.
S17
345
346
347
348
-20 0 20 40 60 80 100 120 140 1600.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
Nitr
ite/m
M
Time/h
NAu-2 pH 8 (HEPES) SWy-2 pH 8 (HEPES) NAu-2 pH 6.1 (PIPES) SWy-2 pH 6.1 (PIPES)
Fig. S3. Negligible amounts of abiotic nitrite reduction by clay-associated Fe(II) at pH 6 and pH
8.
S18
349
350
351
352
Fig. S4 Time-course change of aqueous Fe2+ concentration in the supernatant of bio-oxidation
experiments with clay-associated Fe(II). Total Fe(II) concentration is shown in Fig. 1A, D, and
G.
S19
353
354
355
356
357
358
0 2 4 6Time (d)
0.0
0.2
0.4
0.6
Bio
mas
s (m
gkg
1)
B
0
5
10
Fe2+
(mM
)
1
2
3
4
Nitr
ate
(mM
)
A
Fe2+
Nitrate
Fig. S5. Variations in the concentrations of Fe(II) and nitrate (A), and biomass (B) during the
growth of strain 2002 in laboratory batch reactors. Data points are from a previous study (Weber
et al., 2006) and lines are the modeling results.
S20
359
360
361
362
363
364
Fig. S6 TEM images for SWy-2 at pH 8 after Fe(II) sorption (A) and after bio-oxidation (B): A)
before oxidation, amorphous nanoparticles are located on the edge of clay; B) after bio-
oxidation, goethite are still present with a bundle-shaped morphology, but the nanoparticles are
absent.
S21
365
366
367
368
369
370
Fig. S7 Room temperature (RT, A) and 150 K (B-E) Mössbauer spectra of pristine, Fe(II)-
sorbed, and Fe(II)-sorbed, bio-oxidized NAu-2 samples at pH 6 and pH 8.
S22
371
372
373
Fig. S8 150-K Mössbauer spectra of pristine (A), Fe(II)-sorbed (B), and Fe(II)-sorbed, bio-
oxidized SWy-2 (C) samples at pH 6. At pH 8, Mössbauer spectra for the latter two samples are
shown (D and E, respectively).
S23
374
375
376
377
378
References
Amonette J. E. and Templeton J. C. (1998) Improvements to the quantitative assay of nonrefractory minerals for Fe (II) and total Fe using 1, 10-phenanthroline. Clays Clay Miner. 46, 51–62.
Fell D. A. (1992) Metabolic control analysis: a survey of its theoretical and experimental development. Biochem. J. 286, 313–330.
Jaisi D. P., Liu C., Dong H., Blake R. E. and Fein J. B. (2008) Fe2+ sorption onto nontronite (NAu-2). Geochim. Cosmochim. Acta 72, 5361–5371.
Latta D. E., Neumann A., Premaratne W. A. P. J. and Scherer M. M. (2017) Fe(II)–Fe(III) Electron Transfer in a Clay Mineral with Low Fe Content. ACS Earth Space Chem. 1, 197–208.
Neumann A., Olson T. L. and Scherer M. M. (2013) Spectroscopic Evidence for Fe(II)–Fe(III) Electron Transfer at Clay Mineral Edge and Basal Sites. Environ. Sci. Technol. 47, 6969–6977.
Neumann A., Wu L., Li W., Beard B. L., Johnson C. M., Rosso K. M., Frierdich A. J. and Scherer M. M. (2015) Atom Exchange between Aqueous Fe(II) and Structural Fe in Clay Minerals. Environ. Sci. Technol. 49, 2786–2795.
Schaefer M. V., Gorski C. A. and Scherer M. M. (2011) Spectroscopic Evidence for Interfacial Fe(II)−Fe(III) Electron Transfer in a Clay Mineral. Environ. Sci. Technol. 45, 540–545.
Tsarev S., Waite T. D. and Collins R. N. (2016) Uranium Reduction by Fe(II) in the Presence of Montmorillonite and Nontronite. Environ. Sci. Technol. 50, 8223–8230.
Weber K. A., Picardal F. W. and Roden E. E. (2001) Microbially Catalyzed Nitrate-Dependent Oxidation of Biogenic Solid-Phase Fe(II) Compounds. Environ. Sci. Technol. 35, 1644–1650.
Weber K. A., Pollock J., Cole K. A., O’Connor S. M., Achenbach L. A. and Coates J. D. (2006) Anaerobic Nitrate-Dependent Iron(II) Bio-Oxidation by a Novel Lithoautotrophic Betaproteobacterium, Strain 2002. Appl. Environ. Microbiol. 72, 686–694.
Zhao L., Dong H., Edelmann R. E., Zeng Q. and Agrawal A. (2017) Coupling of Fe(II) oxidation in illite with nitrate reduction and its role in clay mineral transformation. Geochim. Cosmochim. Acta 200, 353–366.
Zhao L., Dong H., Kukkadapu R., Agrawal A., Liu D., Zhang J. and Edelmann R. E. (2013) Biological oxidation of Fe(II) in reduced nontronite coupled with nitrate reduction by Pseudogulbenkiania sp. Strain 2002. Geochim. Cosmochim. Acta 119, 231–247.
S24
379
380381382
383384
385386
387388
389390391
392393394
395396
397398
399400401
402403404
405406407
408409410
S25
411