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Stable carbon isotope fractionation during 1,2-dichloropropaneto-propene transformation by an enrichment culture containing Dehalogenimonas strains and a dcpA gene Lucía Martín-González, Siti Hatijah Mortan, Mònica Rosell, Eloi Parladé, Maira Martínez-Alonso, Nuria Gaju, Gloria Caminal, Lorenz Adrian, and Ernest Marco-Urrea Environ. Sci. Technol., Just Accepted Manuscript • DOI: 10.1021/acs.est.5b00929 • Publication Date (Web): 25 Jun 2015 Downloaded from http://pubs.acs.org on June 29, 2015
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TOC/Abstract art
1 2
Dehalogenimonas growth (qPCR)
Cl Cl C C C
3
1,2-dichloropropane
Detection of 1,2-DCPreductase gene dcpA
ε=-15.0 ± 0.7‰
C C C Propene
4 5 6 7 8 9 10
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Stable carbon isotope fractionation during 1,2-dichloropropane-
12
to-propene transformation by an enrichment culture containing
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Dehalogenimonas strains and a dcpA gene
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14 15 16
L. Martín-González1, S. Hatijah Mortan1, M. Rosell2, E. Parladé3, M. Martínez-Alonso3,
17
N. Gaju3, G. Caminal4, L. Adrian5, E. Marco-Urrea*,1
18 19
1
20
Carrer de les Sitges s/n, 08193 Bellaterra, Spain.
Departament d'Enginyeria Química, Universitat Autònoma de Barcelona (UAB),
21 22
2
23
Geologia, Universitat de Barcelona (UB), Martí Franquès s/n, 08028. Barcelona, Spain.
Departament de Cristal·lografia, Mineralogia i Dipòsits Minerals, Facultat de
24 25
3
26
Bellaterra, Spain.
Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193
27 28
4
29
Barcelona, Spain.
Institut de Química Avançada de Catalunya (IQAC) CSIC, Jordi Girona 18-26, 08034
30 31
5
32
Germany.
Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig,
33 34
*
Phone: +34 5812694; fax: +34 5812013; e-mail:
[email protected].
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ABSTRACT
37 38
A
stable
enrichment culture
39
stoichiometrically dechlorinated 1,2-dichloropropane (1,2-DCP) to propene. Sequential
40
transfers in defined anaerobic medium with the inhibitor bromoethanesulfonate
41
produced a sediment-free culture dechlorinating 1,2-DCP in the absence of
42
methanogenesis. Application of previously published genus-specific primers targeting
43
16S rRNA gene sequences revealed the presence of a Dehalogenimonas strain, and no
44
amplification was obtained with Dehalococcoides-specific primers. The partial
45
sequence of the 16S rRNA amplicon was 100% identical with Dehalogenimonas
46
alkenigignens strain IP3-3. Also, dcpA, a gene described to encode a corrinoid-
47
containing 1,2-DCP reductive dehalogenase was detected. Resistance of the
48
dehalogenating activity to vancomycin, exclusive conversion of vicinally chlorinated
49
alkanes, and tolerance to short-term oxygen exposure is consistent with the hypothesis
50
that a Dehalogenimonas strain is responsible for 1,2-DCP conversion in the culture.
51
Quantitative
52
Dehalogenimonas 16S rRNA genes copies in the culture and consumption of 1,2-DCP.
53
Compound specific isotope analysis revealed that the Dehalogenimonas-catalyzed
54
carbon isotopic fractionation (ǫCbulk) of the 1,2-DCP-to-propene reaction was -15.0 ±
55
0.7‰ under both methanogenic and non-methanogenic conditions. This study
56
demonstrates that carbon isotope fractionation is a valuable approach for monitoring in
57
situ 1,2-DCP reductive dechlorination by Dehalogenimonas strains.
PCR
showed
a
derived
positive
from
Besòs river estuary sediments
correlation
between
the
number
of
58
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1. INTRODUCTION
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1,2-dichloropropane (1,2-DCP) has been used predominantly as a chemical intermediate
62
in the production of tetrachloromethane (carbon tetrachloride) and perchloroethene, lead
63
scavenger for antiknock fluids and solvent. According to the National Primary Drinking
64
Water Regulations established by the U.S. Environmental Protection Agency (EPA), 1
65
1,2-DCP can increase risk of cancer so a maximum contaminant level in drinking water
66
of 5 µg L-1 is legally set for public water systems. Today, 1,2-DCP is a risk for the
67
environment and drinking water quality especially at historically contaminated sites.
68
Under aerobic conditions, 1,2-DCP can be partially co-metabolized to less-
69
chlorinated alkanes. For instance, Pseudomonas sp. strain DCA1 oxidized co-
70
metabolically 1,2-DCP to 2,3-dichloro-1-propanol and 2-chloroethanol during growth
71
on 1,2-dichloroethane2. However, 1,2-DCP exerted a strong inhibitory effect on the
72
growth of this Pseudomonas strain, probably due to a transient toxic intermediate.2
73
Similarly, resting cells of the methanotroph Methylosinus trichosporium OB3b
74
expressing soluble methane monooxygenase catalyzed the transformation of 1,2-DCP to
75
2,3-dichloro-1-propanol, 1-chloro-2-propanol and 2-chloro-1-propanol.3 So far,
76
complete dechlorination of 1,2-DCP to propene or propane has only been demonstrated
77
for organohalide respiring bacteria (OHRB), which use halogenated compounds as
78
terminal electron acceptors during electron transport-based energy conservation.4 To
79
date, few isolated OHRB have been described to derive energy for growth from
80
dechlorination of 1,2-DCP, including Dehalogenimonas alkenigignens strain IP3-3,5
81
Dehalogenimonas lykanthroporepellens strain BL-DC-8 and strain BL-DC-9,6
82
Dehalococcoides mccartyi strain RC and strain KS,7 and Desulfitobacterium
83
dichloroeliminans strain DCA1.8 A Dehalobacter strain was involved in the reductive
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dechlorination of 1,2-DCP in a consortium.9 Although these bacteria share several
85
common phenotypic features including growth under anaerobic conditions, the use of
86
halogenated compounds as respiratory electron acceptors and hydrogen as electron
87
donor, isolated Dehalogenimonas strains differ from other 1,2-DCP-transforming
88
isolates in their exclusive utilization of polychlorinated alkanes as halogenated electron
89
acceptors. Recently, a gene designated dcpA was identified as encoding the reductive
90
dehalogenase
91
Dehalococcoides.10
that
catalyzes
the
dechlorination
of
1,2-DCP-to-propene
in
92
Advances in the fundamental understanding of reductive dechlorination
93
reactions can contribute to an improved assessment of these degradation processes in
94
contaminated subsurface environments. In the last 15 years, compound specific stable
95
isotope analysis has shown the potential of using stable isotope fractionation to confirm
96
and quantify in situ bioremediation and elucidate transformation pathways of many
97
pollutants including chlorinated organic contaminants.11,12 Dichloroelimination is
98
reported to be the major transformation process for 1,2-DCP by OHRB.
99
reaction involves the simultaneous removal of two chlorines from adjacent carbon
100
atoms with the formation of a carbon-carbon double bound, leading to the production of
101
propene from 1,2-DCP. The transformation of 1,2-DCP to propene can proceed via
102
either a stepwise mode (involving a transition state with one C-Cl bond) or a concerted
103
mode (involving the simultaneous cleavage of both C-Cl bonds). In an attempt to
104
elucidate which biochemical mechanism was involved, Fletcher et al.,15 calculated the
105
apparent kinetic isotope effect (AKIE) values simulating both reaction scenarios
106
(stepwise versus concerted mode) from the first carbon isotopic fractionation values (ε)
107
obtained from two different enrichment cultures containing Dehalococcoides mccartyi
108
strains RC and KS. Then the values were compared to the theoretical maximum carbon
8,13,14
This
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primary AKIE (“semiclassical Streitwieser Limits”) for the cleavage of a C-Cl bond.
110
However, the estimated AKIEs assuming stepwise or concerted reaction were not
111
conclusive to demonstrate the reaction mechanism of 1,2-DCP dichloroelimination. The
112
ε values obtained for the two Dehalococcoides mccartyi strains in their respective 1,2-
113
DCP-to-propene consortia were statistically identical (-10.8 ± 0.9‰ and -11.3 ± 0.8‰,
114
respectively).
115
The aim of this study was to get more insight into the microbial processes
116
involved in chloroalkane dechlorination and strengthen the prospect of applying
117
compound specific stable isotope analysis as a tool to demonstrate in situ
118
biodegradation. We established an enrichment culture derived from sediments collected
119
in the Besòs River estuary (Barcelona) that dechlorinates vicinally chlorinated alkanes.
120
This location was chosen because sediments of this coastal area have been historically
121
contaminated with short-chain chlorinated paraffins,16 providing a potential niche for
122
OHRB. Our results demonstrate that Dehalogenimonas spp. were responsible for 1,2-
123
DCP dechlorination and carbon isotopic fractionation differed from that described for
124
Dehalococcoides mccartyi strains although the dcpA gene involved in the 1,2-DCP-to-
125
propene transformation in Dehalococcoides strains was also present in our culture.
126 127
2. MATERIALS AND METHODS
128 129
2.1. Sampling and cultivation
130
Inocula were taken from sediments of the Besòs river estuary (Spain). The samples were
131
collected from layers 15 cm below the surface. Sediments were transported to the lab,
132
transferred to an anaerobic glovebox and used to set up microcosms on the same day.
133
Each microcosm consisted of 6 g of sediment (wet weight) in 100 mL glass serum
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bottles containing 65 mL of a sterilized anaerobic synthetic medium previously used to
135
grow Dehalococcoides mccartyi strain CBDB1.17 It contained vitamins, trace elements,
136
5 mM sodium acetate as carbon source, and as reducing agent either 0.8 mM titanium
137
(III) citrate (0.8 mM titanium (III), 1.6 mM citrate) or Na2S × 9 H2O and L-cysteine (0.2
138
mM each), as indicated. The serum bottles were sealed with Teflon-coated butyl rubber
139
septa and aluminum crimp caps and gassed with N2/CO2 (4:1, v/v, 0.2 bar overpressure)
140
and H2 (added to an overpressure of 0.4 bar). 1,2-DCP was added with a syringe from a
141
3.2 mM stock solution in acetone to a nominal concentration of 50 µM. Microcosms
142
were prepared at least in triplicate and incubated at 25 ºC in the dark in static
143
conditions. Microcosms that depleted the initial dose of 1,2-DCP were reamended with
144
the same amount of the electron acceptor and transferred to fresh medium (10% v/v)
145
when approximately 80% of the initial dose of 1,2-DCP was consumed.
146
For isotopic analysis, several parallel incubations from the same inoculum were
147
prepared at the same time and sacrificed at different time points. Three types of controls
148
were included at least in duplicate: i) controls containing heat-killed inoculum and 1,2-
149
DCP, ii) live controls without 1,2-DCP, and iii) abiotic controls containing the growth
150
medium with 1,2-DCP without inoculum, to control losses, abiotic transformations, and
151
the transfer of compounds from previous degradation experiment with the inoculum or
152
potential impurities from the stock solution, respectively.
153 154
2.2. Analytical methods
155
Chlorinated compounds, propene and methane were detected by analyzing 0.5 mL
156
headspace samples respectively taken with a 1.0 mL pressure-lock precision analytical
157
syringe (Vici, USA) from the serum bottles. All compounds were identified using
158
retention times of chemical standards. A gas chromatograph (GC) model 6890N
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(Agilent Technologies; Santa Clara, CA, USA) equipped with a DB-624 column (30 m
160
× 0.32 mm with 0.25 µm film thickness; Agilent Technologies) and a flame ionization
161
detector (FID) was used to analyze all volatile organic compounds. Helium was used as
162
the carrier gas (0.9 mL min-1). The injector and detector temperatures were set at 250 °C
163
and 300 °C respectively. After the injection of the sample (split ratio=2), the initial oven
164
temperature (35 °C) was held for 3 min and then ramped at 10 °C min-1 to 240 °C,
165
which was held for 4 min. Peak areas were calculated using Millennium/Empower
166
software (Waters, Milford, MA, USA). Calibration was based on aqueous standards,
167
with the same liquid and headspace volumes as in the microcosms. Results are
168
presented as nominal concentrations (µmol L-1 of liquid volume). Propene was analyzed
169
using an identical GC-FID equipped with a HP Plot Q column (30 m × 0.53 mm with 40
170
µm film thickness, Agilent Technologies). The oven temperature was fixed at 150 ºC,
171
the injector temperature at 250 ºC and the detector temperature at 260 ºC. Run time
172
lasted 6 minutes.
173
Methane concentration was analyzed using a GC HP 5890 (Agilent
174
Technologies, Palo Alto, USA) with a thermal conductivity detector (TCD) equipped
175
with a Porapack Q column (3 m x 3.2 mm, Sigma-Aldrich, Barcelona, Spain) using
176
helium at 338 kPa as the carrier gas. The oven temperature was fixed at 70 ºC, the
177
injector temperature at 150 ºC and the detector temperature at 180 ºC. Run time was 3
178
minutes.
179
When needed, identification of transformation products was done using a gas
180
chromatograph equipped with a mass selective detector (Agilent 5975C + 7890 Series
181
GC-MS). Compounds were separated using a DB-624 column (60 m × 0.25 mm, film
182
thickness 1.4 µm, Agilent Technologies). Carrier gas was helium at a flow rate of 0.8
183
mL min-1. The temperature was hold for 2 min at 50 °C, raised to 170 °C at a rate of 3 9 ACS Paragon Plus Environment
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°C min-1 and finally to 230 ºC at a rate of 8 °C min-1. The transfer line to the mass
185
spectrometer was maintained at 235 °C. Mass spectra were obtained after ionization by
186
electronic impact at 70 eV and at a multiplier voltage of 1379 V. Data was collected at
187
m/z values between 33 and 300. Mass spectra obtained were compared with the NIST
188
98 MS Library Database and with the generated mass spectra of standards.
189
Diclofenac and triclosan concentrations were measured using high performance
190
liquid chromatography (HPLC). Liquid samples (1 mL) from experimental bottles were
191
diluted 1:1 (v:v) with acetone as a solvent before mixing on a vortex (Zx3,Velp
192
Scientifica, Italy). Next, the samples were filtered (Millex-GV, PVDF, 0.22 µm,
193
Millipore) and analysed using a Dionex 3000 Ultimate HPLC (Barcelona, Spain) that
194
was equipped with a UV detector at 277 nm. The column temperature was 30 ºC, and a
195
sample volume of 10 µL was injected from a Dionex autosampler. Chromatographic
196
separation was achieved using a GraceSmart RP-18 column (250 x 4.6 mm, particle size
197
of 5 µm). The mobile phase consisted of a 0.1% formic acid solution (A) and
198
acetonitrile (B). The analysis was performed isocratically (30% A) at 1 mL min-1. The
199
retention times for diclofenac and triclosan were 4.3 min and 5.4 min, respectively. The
200
quantification limit for both compounds was 2 mg L-1.
201
The presence of bromide ions was evaluated on a Dionex ICS-2000 ion
202
chromatography system equipped with an IonPac AS18 anion-exchange column. The
203
column was operated at a temperature of 30 °C and a flow rate of 1 mL min-1. The
204
injection volume was 25 µL. The potassium hydroxide concentration of the eluent
205
varied from 25 mM to 50 mM along the 10 min analysis.
206
For isotopic analysis, 6 mL of NaOH was added to parallel incubations to stop
207
biological transformations at different time points and bottles were preserved at 4ºC
208
until analysis. Carbon isotope analyses of propene and 1,2-DCP were performed using a
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Agilent 6890 gas chromatograph (Palo Alto, CA, USA) equipped with a split/splitless
210
injector, coupled to a Delta Plus isotope ratio mass spectrometer through a GC-
211
Combustion III interface (ThermoFinnigan, Bremen, Germany). A headspace gas
212
sample with a volume between 0.6 and 1 mL, depending on propene concentration
213
measured previously, was injected by a gas syringe. For propene, the GC was equipped
214
with a HP-PLOT/Q column (30 m x 0.32 mm, 20 µm film thickness, Agilent
215
Technologies, Palo Alto, CA, USA). The injector was set at 220 ºC in split mode (1:10).
216
The oven temperature program was kept at 40 °C for 10 min, heated to 220 °C at a rate
217
of 15 °C min-1 and finally held at 220 °C for 10 min. Helium was used as a carrier gas
218
with a gas flow rate of 1.2 mL min-1. The retention time of propene was identified by
219
injecting 300 µL of a standard gas mixture (Supelco Scotty Analyzed Gases, C2-C6
220
Olefins, Sigma-Aldrich, St. Louis, Missouri, USA) containing ethene, propene, 1-
221
butene, 1-pentene, 1-hexene each at 100 mg L-1. Once the δ13C of propene was
222
analyzed, liquid aliquots were removed from the experimental bottles and placed in 20-
223
mL vials filled with 10-mL aqueous phase (samples were diluted or not in Milli-Q water
224
depending on the 1,2-DCP concentration) and containing a 30 mm PTFE-coated stir
225
bar. This solution was stirred at room temperature and 1,2-DCP was extracted during 20
226
minutes by headspace solid-phase micro-extraction (HS-SPME) using a manual sampler
227
holder equipped with a 75-µm Carboxen-PDMS fiber (Supelco, Bellefonte, PA, USA).
228
For 1,2-DCP, the GC was equipped with a Supelco SPB-624 column (60 m × 0.32 mm,
229
1.8 µm film thickness; Bellefonte, PA, USA). The injector was set at 220 ºC in split
230
mode (1:10). The oven temperature program was kept at 60 °C for 2 min, heated to 220
231
°C at a rate of 8 °C min-1 and finally held at 220 °C for 5 min. Helium was used as a
232
carrier gas with a gas flow rate of 1.8 mL min-1. Several 1,2-DCP aqueous control
233
standards were prepared daily from the same pure 1,2-DCP standard which was also
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used for the cultures (standard stock solutions were prepared first in HPLC grade
235
methanol) and analyzed on the same days as the samples to ensure accuracy of the
236
isotopic measurements. All the controls injected in different replicas, days and
237
concentrations (from 30 to 300 µg L-1) had an average 1,2-DCP-δ13C values of -29.3 ±
238
0.5‰ (n = 34).
239
Carbon isotope ratios are reported in delta notation (δ13C) relative to an international
240
standard (VPDB, Vienna Pee Dee Belemnite) and expressed in parts per mil (‰)
241
13 ‰ =
− 1 × 1000
are the isotope ratios (13C/12C) of the sample and the standard,
242
Where
243
respectively. A simplified Rayleigh equation for a closed system was used to quantify
244
the isotopic fractionation:11
245
and
(1)
ɛ ln = ln 0 0 1000
(2)
246
where the isotopic fractionation (ε) describes the relationship between changes in
247
carbon isotopic composition
248
concentrations (C) along the time course (t) with respect to the initial concentration (0).
249
Most of the measurements were run in duplicate, and the one standard deviation (1σ) of
250
the δ13C values obtained was below or equal to ±0.5‰.18
251
Position-specific carbon isotopic fractionation (ǫreactive) values, which are corrected for
252
the presence of nonreactive positions, were calculated for both stepwise and concerted
253
reactions according to Elsner et al.11 as done by Fletcher et al.15, where n is the number
254
of carbon atoms in the molecule (in the case of 1,2-DCP, n =3) and x is the number of
255
carbon atoms in the reactive position (in the case of a stepwise reaction, x = 1 and in the
256
case of a concerted reaction, x = 2) by plotting again the modified Rayleigh equation:
⁄0 = 13 + 1000 ⁄ 13 0 + 1000
and the
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1000 + 13 0 + "⁄# ∆ 13 ɛ& '() ln ! %= ln 13 0 1000 + 0 1000
(3)
259
Then, the apparent kinetic carbon isotope effect (AKIE) for each case was calculated
260
according to:
261
*+,- = 1⁄.1 + / × ɛ& '() ⁄1000 0
(4)
262
where z, the number of indistinguishable reactive sites, is a correction for the effects of
263
intramolecular competition (in the case of 1,2-DCP, z = 1).
264
Carbon isotopic mass balance and the associated concentration-weighted average
265
δ13Csum is calculated similar to the sequential reductive dechlorination of chlorinated
266
ethenes19,20 but only considering 1,2-DCP as parental compound and propene as final
267
product:
268
13 1 ‰ = #1,2−45 13 1,2−45 + #&6" 13 &6"
(5)
269
where x is the molar fraction of each compound relative to the total molar mass (1,2-
270
DCP plus propene) at each time. If propene is not further transformed, the δ13Csum
271
remains constant over the 1,2-DCP dichloroelimination. As a certain amount of propene
272
was transferred with the inoculum from the previous experiment (initial propene
273
detected and quantified in live controls without 1,2-DCP), the
274
corresponding to newly generated propene in equation 5 was calculated as follows:
275
13 &6" =
13 1&
&6"
− #("((
#7"&
&6"
&6"
13 ("((
&6"
(6)
276 277
2.3. DNA extraction and PCR
278
Genomic DNA was extracted from 50 mL of the consortium using an UltraClean water
279
DNA isolation kit (MoBio, Carlsbad, CA). Amplification of bacterial 16S rRNA genes
280
was conducted with two sets of primers. The first primer combination (BL-DC-142f and
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BL-DC-1351r) was specific for the genus Dehalogenimonas.21 The second primer set
282
specifically targeted the genus Dehalococcoides (Dch1F and Dch264R).22 Genomic
283
DNA was also analyzed for the presence of the dcpA gene. Primers dcpA-360F and
284
dcpA-1449R10 designed for conventional PCR were used. Genomic DNA from
285
Dehalogenimonas lykanthroporepellens strain BL-DC-9 (=ATCC BAA-1523 = JCM
286
15061) and Dehalococcoides mccartyi strain CBDB1 were used as positive controls.
287
Each 50 µL reaction mixture contained 50 ng of template DNA, 1x PCR buffer (20 mM
288
Tris/HCl, pH 8.4, 50 mM KCl), 1.5 mM MgCl2, 200 µM of each deoxynucleoside
289
triphosphate, 0.5 µM of each primer and 2.5 U of Taq DNA polymerase (Invitrogen,
290
Carlsberg, CA, USA). The thermal programs used for PCR amplification of
291
Dehalogenimonas and dcpA gene were previously described.10,21 For primer set Dch1F
292
and Dch264R, the program used an initial denaturation at 95 °C for 5 min and then 35
293
cycles at 95°C for 30 s, the desired annealing temperature (59 °C) for 30 s, and
294
extension at 72°C for 60 s, followed by a final extension step at 72 °C for 7 min.
295
Amplicons were analyzed by electrophoresis in a 2 % (wt/v) agarose gel at 75 V for 40
296
min. Primers used in the second amplification in the nested PCR approach were 341f-
297
GC and 907r. Temperature cycling was done as described previously.23 Sequences of
298
the different oligonucleotide primer sets used in this study are given in Table S2.
299 300
2.4 Denaturing Gradient Gel Electrophoresis (DGGE) analysis and sequencing
301
Five-hundred ng of PCR product from nested PCR using the primer sets BL-DC-
302
142f/BL-DC-1351r and 341f-GC/907r were loaded onto a denaturing gradient gel.
303
DGGE was carried out using a Bio-Rad DCode system, as described,23 in a 6%
304
polyacrylamide gel with 30-70% denaturant gradient (100% denaturant contained 7 M
305
urea and 40% v/v deionized formamide). Electrophoresis was performed at 60 ºC with a
306
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mL-1), then inspected under UV illumination and photographed. Prominent bands were
308
excised from the gels, reamplified, and then purified using the PCR Clean up Kit
309
(MoBio Laboratories) for subsequent sequencing.
310
Sequencing reactions were performed by Macrogen (South Korea) using the Big Dye
311
Terminator v3.1 sequencing kit; reactions were run in an automatic capillary type ABI
312
3730XL analyzer-96. Sequences were first screened to detect potential chimeric
313
artifacts
314
(http://www.mothur.org/wiki/Download_mothur)24 and then compared to those
315
deposited in the GenBank nucleotide database using the BLASTN program.25 The 16S
316
rRNA gene sequences determined in this study are available at the GenBank database
317
under accession numbers KP780280 through KP780282. Each band designation
318
includes a code specifying its origin (BREd, Besòs River Estuary Dehalogenimonas)
319
followed by a number indicating the order in which the sequence was isolated from the
320
gel.
using
the
Chimera.uchime
program
in
Mothur
1.33.3
321 322
2.5 Quantitative PCR (qPCR)
323
The qPCR assays were performed with DNA extracted from cultures growing in
324
parallel consuming different amounts of 1,2-DCP. Primer set mod-BL-DC-1243f and
325
BL-DC-1351r21 was used in qPCR to quantify Dehalogenimonas 16S rRNA gene
326
copies in the consortia. qPCR was performed using a CFX96 Real-Time System (Bio-
327
Rad) in 20 µL total reaction volumes containing 1x ssoAdvanced Universal SYBR®
328
Green Supermix (Bio-Rad), 0.5 µM of each primer and 36 ng of sample DNA. The
329
amplification program used was reported previously.21 A melting curve analysis to
330
assess product specificity followed each PCR reaction. Melting curves were generated
331
from 65 to 95 ºC with increments of 0.5 ºC each cycle and a dwell time at each
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332
temperature of 5 s. Samples and non-template controls were analyzed in triplicates and
333
the latter were included in each assay. Each calibration curve was prepared using
334
purified PCR product of a partial 16S rRNA gene (1199 bp) from Dehalogenimonas
335
lykanthroporepellens BL-DC-9T. Six serial dilutions were prepared independently in
336
triplicates and concentrations were determined with a NanoDrop spectrophotometer
337
(Thermo Fisher Scientific). Gene copies per qPCR reaction and PCR amplification
338
efficiency were calculated as described previously.26 PCR amplification efficiency
339
ranged from 93.2% to 102.3%.
340 341
3. RESULTS AND DISCUSSION
342
3.1. Enrichment of dehalogenating bacteria
343
Sediments collected from the Besòs river estuary were incubated in reduced medium
344
containing 50 µM 1,2-DCP. In the first transfer, hydrogenolysis of 1,2-DCP to 1-
345
chloropropane and minor amounts of 2-chloropropane was the predominant reaction in
346
most of the cultures. Hydrogenolysis of chloroalkanes was an unexpected reaction
347
which has been reported only once before,13 and therefore it was specifically followed.
348
A decrease in the production of chloropropanes in the subsequent transfers was
349
observed, and titanium (III) citrate was replaced by Na2S and L-cysteine (0.2 mM each)
350
in parallel cultures to test whether titanium (III) citrate exerted inhibition to the
351
dechlorinating population catalyzing hydrogenolysis. Production of chloropropanes was
352
favored in the cysteine-sulfide medium but after the fourth transfer hydrogenolytic
353
activity was lost and propene became the unique identified transformation product.
354
Although we corroborated that hydrogenolysis of chloropropanes is possible, the
355
identity and characteristics of the bacteria catalyzing this process remained unknown.
356
Similarly to the results showed by Löffler et al.,13 hydrogenolysis was not observed in 16 ACS Paragon Plus Environment
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357
sediment-free cultures, which is consistent with the hypothesis that microorganisms
358
catalyzing this reaction may be favored in sedimentary environments.
359
Dihaloelimination of 1,2-DCP to propene was sustained in subsequent transfers
360
inoculating 10% (v/v) from the original microcosms using the L-cysteine-sulfide
361
reducing agent. A sediment-free culture was obtained after five consecutive transfers of
362
the supernatant to fresh medium. The repeated addition of 1,2-DCP led to faster
363
dechlorination rates suggesting that dichloroelimination was supporting growth of the
364
dechlorinating bacteria (Fig. S1A). The stoichiometric relationship between 1,2-DCP
365
consumed and propene produced revealed a closed molar balance and excluded the
366
production of alternative metabolites (Table S1). Neither dechlorination of 1,2-DCP nor
367
propene production were detected in the abiotic and heat-killed controls indicating that
368
the reaction was biotically mediated.
369
As shown in Fig. S1A, methane was produced parallel with the dechlorination of
370
1,2-DCP. To investigate the role of methanogens in dichloroelimination of 1,2-DCP, we
371
tested the effect of bromoethanesulfonate (BES) at two different concentrations (5 and
372
25 mM) and of 1,2-dibromopropane (10 µM) on dechlorination activity. The latter was
373
initially tested as a possible electron acceptor (see below) but instead of that, we
374
observed that it completely inhibited methane production in our cultures. Methane
375
production was not inhibited at 5 mM BES , but it completely ceased at a concentration
376
of 25 mM with no negative effect on dechlorinating activity (Fig. S1B). Addition of 10
377
µM of dibromopropane completely inhibited both methanogenic activity and 1,2-DCP
378
dechlorination. The addition of vancomycin (5 mg L-1), an inhibitor of peptidoglycan
379
cell-wall biosynthesis, provoked an increase in the dichloroelimination rate of 1,2-DCP.
380
The consortia containing vancomycin were transferred for more than eleven subsequent
381
transfers (10% v/v) without losing this dechlorinating activity.
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382 383
3.2. Dehalogenation of alternative electron acceptors
384
Besides 1,2-DCP, we tested the potential of the consortium to reductively dechlorinate
385
various
386
dichloroethane,
387
(tetrachloroethene,
388
(monochlorobenzene, 1,2,4-trichlorobenzene, diclofenac, and triclosan), bromoalkanes
389
(1,6-dibromohexane, 1,2-dibromopropane) and chloroform by adding them at a
390
concentration between 5 and 50 µM. After one month of incubation, the concentrations
391
of the halogenated compounds were analyzed by GC. Debromination activity was tested
392
by measuring bromide concentration by ion chromatography. Dehalogenation was only
393
observed in cultures containing vicinally chlorinated alkanes. Thus, 1,2,3-
394
trichloropropane was converted to allyl chloride and allyl alcohol; 1,1,2-trichloroethane
395
was converted to vinyl chloride; and 1,2-dichloroethane to ethene.
chlorinated
alkanes
(1,2,3-trichloropropane;
1-chloropropane
and
trichloroethene,
1,1,2-trichloroethane;
2-chloropropane),
chlorinated
trans-dichloroethene),
1,2-
alkenes
chloroaromatics
396 397
3.3. Identification of Dehalogenimonas spp and the dcpA gene
398
To
399
Desulfitobacterium and Dehalobacter) have been implicated in the dechlorination of
400
1,2-DCP to propene. The presence of OHRB belonging to the genus Dehalobacter and
401
Desulfitobacterium in our cultures was ruled out because they cannot grow in the
402
presence of vancomycin. In addition, morphological evidence supported the
403
involvement of either Dehalogenimonas or Dehalococcoides since microscopic
404
observations of cultures fed with several 1,2-DCP additions showed predominantly
405
irregular cocci, but not rod-shaped cells as those described for Desulfitobacterium and
406
Dehalobacter spp (data not shown). In order to determine if known OHRB were present
date,
four
OHRB
populations
(Dehalogenimonas,
Dehalococcoides,
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407
in the dehalogenating consortium we performed PCR reactions with genus-specific
408
primers for Dehalococcoides and Dehalogenimonas 16S rRNA. The tested PCR primers
409
targeting for Dehalococcoides spp failed to produce an amplicon, but confirmed the
410
presence of Dehalogenimonas spp in our culture (Fig. S2A and S2B). Furthermore,
411
nested PCR followed by DGGE allowed the visualization of a prominent band (Fig. S3).
412
Several band replicates were excised from the gel, sequenced, and partial 16S rRNA
413
gene sequences obtained (accession numbers from KP780280 to KP780282) showed
414
100% identity with Dehalogenimonas alkenigignens strain IP3-3.
415
The
hypothesis
that
Dehalogenimonas
strains
are
involved
in
the
416
dichloroelimination of 1,2-DCP in these enrichment cultures was consistent with three
417
complementary lines of evidence. First, we tested the oxygen tolerance of the OHRB
418
contained in our culture by exposing the inoculum to air until the redox indicator
419
resazurin turned pink, and afterwards it was injected into fresh reduced medium. These
420
cultures grew at the same dechlorination rate than positive controls not exposed to
421
oxygen, which is consistent with the oxygen tolerance observed for Dehalogenimonas14
422
but disfavors the involvement of Dehalococcoides species due to their strong sensitivity
423
to short-term oxygen exposure.22 We repeated the short-time exposure of the inoculum
424
to oxygen for three serial transfers with identical results. Secondly, the OHRB present
425
in our culture solely dechlorinate vicinally chlorinated alkanes. This strong substrate
426
specialization is one of the remarkable characteristics observed for Dehalogenimonas
427
strains.5,6 Although it has been described by others that growth of a Dehalogenimonas
428
population in a consortium was coupled to reductive dechlorination of trans-
429
dichloroethene to vinyl chloride,22 our culture could not transform chlorinated ethenes
430
within one month of incubation. Thirdly, we monitored the abundance of
431
Dehalogenimonas 16S rRNA gene copies using quantitative PCR (qPCR) to determine
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432
whether 1,2-DCP dechlorination was coupled to Dehalogenimonas growth in the Besòs
433
river cultures. The addition of several successive doses of 1,2-DCP when all the
434
electron acceptor was consumed (Fig. 1A) resulted in a concomitant increase in the
435
number of Dehalogenimonas 16S rRNA gene copies detected in the cultures (Fig. 1B).
436
No growth was observed in control cultures that received no 1,2-DCP, showing that 1,2-
437
DCP dechlorination was a growth-linked respiratory process. These findings were
438
consistent with the detection of the dcpA gene encoding 1,2-DCP reductive
439
dehalogenase in Dehalogenimonas strain BL-DC-9, Dehalococcoides mccartyi strain
440
RC and strain KS.10 As shown in Fig. S2C, a conventional PCR using dcpA-360F and
441
dcpA-1449R primers confirms the presence of a unique amplicon of the expected size
442
(1089 bp) when applied to genomic DNA from the consortium.
443 444
3.4. Effect of methanogenic activity on 1,2-DCP fractionation
445
Methanogenic archaea are often present in dehalogenating communities and compete
446
with OHRB for hydrogen and acetate, but some populations can also synthesize
447
corrinoids de novo that can be used by corrinoid auxotrophs such as Dehalogenimonas
448
spp. Previous studies have shown that the metabolism of OHRB can be altered by
449
supplying different forms of corrinoids i.e. cyanocobalamin added exogenously to the
450
medium or corrinoids supplied by a methanogenic enrichment culture.28 Therefore, here
451
we aimed to investigate whether the presence of methanogens may exert an effect on the
452
isotopic fractionation of 1,2-DCP due to the corrinoid source or due to corrinoid
453
concentration. In addition, the results may help to identify a yet unperceived
454
concomitant cometabolic transformation of 1,2-DCP. This information is of importance
455
to interpret and increase confidence in the isotopic fractionation data collected from the
456
field since growth of OHRB is mostly favored in methanogenic zones. Therefore,
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457
carbon isotopic composition and concentration of 1,2-DCP was monitored in
458
methanogenic (fifth transfer) and non-methanogenic enrichment cultures (eleventh
459
transfer) containing 25 mM BES during 1,2-DCP dechlorination. In methanogenic
460
cultures, 94% of 1,2-DCP was transformed to propene within 13 days, whereas non-
461
methanogenic cultures were much slower and only 77% transformation was reached
462
after 21 days. In both methanogenic and non-methanogenic cultures, 1,2-DCP was
463
significantly enriched in
464
considered carbon isotopic compositions of spiked 1,2-DCP was -29.1 ± 0.5‰ and -
465
29.8 ± 0.3‰, respectively for the two experiments, and were calculated from the
466
average delta value obtained from aqueous control standards injected together with the
467
samples. These values did not differ significantly from each other (within their 1σ) nor
468
to the ones obtained in abiotic controls after the incubation period (-29.2 ± 0.2‰ and -
469
29.9 ± 0.1‰, respectively for each series). Therefore, the equilibrium of 1,2-DCP
470
between headspace and liquid in the serum bottles did not affect substantially the
471
measured 1,2-DCP delta value. However, in methanogenic cultures, the inoculum
472
contained a low concentration of residual 13C-enriched 1,2-DCP. This resulted in a more
473
13
474
2). In non-methanogenic cultures, no 1,2-DCP was detected in live controls without 1,2-
475
DCP, demonstrating that no enriched 1,2-DCP was transferred with the inoculum and
476
the -29.9 ± 0.1‰ value from abiotic controls was used as initial (δ13C0). Taking this into
477
account, 1,2-DCP carbon isotope fractionation (εCbulk) was calculated with the Rayleigh
478
equation (equation 2) for methanogenic (-15.3 ± 0.7‰) and non-methanogenic (-13.7 ±
479
2.0‰) enrichment cultures (Table 1). These values were statistically identical according
480
to their 95% confidence intervals indicating that the reaction mechanism was not
481
detectably affected by the presence/absence of methanogens in our consortium. Our
13
C during the transformation to propene (Figure 2). The
C-enriched 1,2-DCP initial value (δ13C0) of -27.5 ± 0.1‰ in this experiment (Figure
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482
results are in agreement with those reported recently in which trichloroethene
483
fractionation was not significantly different in two different Dehalococcoides-
484
containing enrichments cultures when methanogenic activity was either inhibited or
485
promoted.29
486 487
3.5. Calculation of carbon isotopic fractionation and AKIE values of 1,2-DCP
488
dechlorination
489
Combined εCbulk (-15.0 ± 0.7‰) was calculated by plotting methanogenic and non-
490
methanogenic data together (Figure 3) giving a correlation factor of 0.991 indicating
491
that dichloroelimation of 1,2-DCP to propene is well described by the Rayleigh model.
492
It is expected that species containing the same reductive dehalogenase produce similar
493
fractionation of 1,2-DCP, as previously observed for Dehalococcoides strains RC and
494
KS (-10.8 ± 0.9‰ and -11.3 ± 0.8‰, respectively).15 However, the obtained 1,2-DCP
495
εCbulk of -15.0 ± 0.7‰ for our Dehalogenimonas-containing culture differs significantly
496
according to 95% confidence intervals. Although this difference is intriguing, it is
497
known that species belonging to the same genus and harboring the same functional
498
dehalogenase can produce significantly different isotopic fractionation of chlorinated
499
compounds.30 This phenomenon is commonly attributed to physiological processes such
500
as transport of substrate across the cell membrane or differences in the active site of the
501
enzyme.
502
To distinguish if dichloroelimination proceeds via a stepwise or concerted mode
503
AKIE values were calculated (equation 4) using the combined carbon isotopic
504
fractionation obtained (Table 1). Assuming that the 1,2-DCP dichloroelimination
505
reaction was stepwise, involving the cleavage of one C-Cl bond in the transition state,
506
the combined εreactive value was -43 ± 2‰ and the corresponding AKIE 1.045 ± 0.002.
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507
Assuming that the reaction was concerted, involving the simultaneous cleavage of both
508
C-Cl bonds, the combined εreactive value was -22 ± 1‰ corresponding to an AKIE value
509
of 1.023 ± 0.001. Therefore, both AKIE values were lower than the theoretical
510
maximum carbon primary KIE (“semiclassical Streitwieser Limits”) for the complete
511
cleavage of a C-Cl bond (1.057).31 However, considering the indication of Elsner et al.
512
2005 that realistic values with transition states at about 50% bond cleavage can be
513
expected to be half as pronounced (AKIE = 1.03),11 the concerted reaction with an
514
obtained AKIE value lower than that (1.023) might be more probable in our case than
515
the stepwise (1.045), whereas for Fletcher et al. 2009 both values were still lower
516
enough (1.017 and 1.033, respectively).15
517
In addition, carbon isotopic composition of propene was measured in non-
518
methanogenic enrichment cultures to confirm the stoichiometric transformation from
519
1,2-DCP by isotopic mass balance. Equation 6 was used to calculate the newly
520
generated propene δ13C value. As shown in Fig. 2, 13C-depleted propene was generated
521
by 1,2-DCP dechlorination confirming isotope fractionation and it was getting
522
significantly enriched along the 1,2-DCP dichloroelimination (δ13Cpropene values from -
523
43.4‰ to -36.3‰). Moreover, by applying equation 5, the concentration-weighted
524
average δ13Csum was nearly constant at -31 ± 1‰ which is not statistically different from
525
the considered initial 1,2-DCP composition in this experiment (-29.8 ± 0.3‰),
526
suggesting a close carbon isotopic mass balance during dichloroelimination.
527
In summary, we established a stable Dehalogenimonas-containing culture that
528
exclusively dechlorinates vicinally chlorinated alkanes. Dechlorination of 1,2-DCP was
529
accompanied by a change in the isotope composition of 1,2-DCP. Production of
530
propene from 1,2-DCP was stoichiometric and also fits with the carbon isotopic
531
balance. The calculated εCbulk was in the same order of magnitude but differs from that
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532
reported for Dehalococcoides mccartyi strain RS and strain KC, although the dcpA gene
533
encoding 1,2-DCP reductive dehalogenase was also identified in our culture. The
534
carbon isotopic factor determined in this study can provide useful information to apply
535
compound specific stable isotope analysis for quantification of in situ dechlorination of
536
1,2-DCP in aquifers.
537 538
ACKNOWLEDGMENTS
539 540
This work has been funded by the Spanish Ministry of Economy and Competitiveness
541
(project CTM2013-48545-C2-1-R) and supported by the Generalitat de Catalunya
542
(Consolidated Research Group 2014-SGR-476). The Department of Chemical
543
Engineering of the Universitat Autònoma de Barcelona (UAB) is member of the Xarxa
544
de Referència en Biotecnologia de la Generalitat de Catalunya. E.M-U is indebted to the
545
UAB APOSTA grant that was critical for initiating this research. M.R. acknowledges
546
support from a Marie Curie Career Integration Grant in the framework of the IMOTEC-
547
BOX project (PCIG9-GA-2011-293808). S.H.M acknowledges support from the
548
Ministry of Education Malaysia (SLAI-UMP Scholarship) for a predoctoral fellowship
549
and L.A. acknowledges support by the DFG (FOR1530). We thank Dr. William M.
550
Moe for providing genomic DNA from Dehalogenimonas lykanthroporepellens BL-
551
DC-9.
552 553
SUPPORTING INFORMATION AVAILABLE
554
Additional tables and figures are included. This information is available free of charge
555
via the Internet at http://pubs.acs.org.
556
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557
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microbial ecology. In Methods in microbiology; Paul, J. H. Ed.; Academic Press:
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London 2001; pp 425.
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[24] Edgar, R. C.; Haas, B. J.; Clemente, J. C.; Quince, C.; Knight R. UCHIME
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improves sensitivity and speed of chimera detection. Bioinformatics. 2011, 27, 2194–
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2200; DOI 10.1093/bioinformatics/btr381.
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[25] Tatusova, T. A.; Madden, T. L. BLAST 2 Sequences, a new tool for comparing
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protein and nucleotide sequences. FEMS Microbiol Lett. 1999, 174, 247-250; DOI
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http://dx.doi.org/10.1111/j.1574-6968.1999.tb13575.x.
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[26] Ritalahti, K. M.; Amos, B. K.; Sung, Y.; Wu, Q.; Koenigsberg, S. S.; Löffler, F. E.
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Quantitative
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simultaneously monitors multiple Dehalococcoides strains. Appl Environ Microbiol.
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2006. 72, 2765–2774; DOI 10.1128/AEM.72.4.2765-2774.2006.
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[27] Löffler, F. E., Yan, J., Ritalahti, K. M., Adrian, L., Edwards, E. A., Konstantinidis,
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K. T., Müller, J. A., Fullerton, H., Zinder, S. H., Spormann, A. M. Dehalococcoides
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mccartyi gen. nov., sp. nov., obligate organohalide-respiring anaerobic bacteria, relevant
653
to halogen cycling and bioremediation, belong to a novel bacterial class,
targeting
PCR
16S
rRNA
targeting
genes
of
the
Dehalogenimonas
16S
rRNA
and
organohalide-respiring
species
reductive
in
the
dehalogenase
genus
1,1,2,2-
genes
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Dehalococcoidetes classis nov., within the phylum Chloroflexi. Int J Syst Evol.
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Microbiol. 2013, 63, 625-635; DOI 10.1099/ijs.0.034926-0.
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[28] Johnson, D. R.; nemir, A.; Andersen, G. L.; Zinder, S. H.; Alvarez-Cohen, L.
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Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides
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ethenogenes
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http://dx.doi.org/10.1111/j.1574-6968.2009.01569.x.
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[29] Harding, K. C.; Lee, P. K.; Bill, M.; Buscheck, T. E.; Conrad, M. E.; Alvarez-
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Cohen, L. Effects of varying growth conditions on stable carbon isotope fractionation of
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trichloroethene (TCE) by tceA-containing Dehalococcoides mccartyi strains. Environ.
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Sci. Technol. 2013, 47, 12342-12350; DOI 10.1021/es402617q.
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[30] Marco-Urrea, E.; Nijenhuis, I.; Adrian, L. Transformation and carbon isotope
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fractionation of tetra- and trichloroethene to trans-dichloroethene by Dehalococcoides
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sp.
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10.1021/es1023459.
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[31] Huskey, W. P. Origins and interpretations of heavy-atom isotope effects. In
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FEMS
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DOI
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671 672 673
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FIGURE LEGENDS
675 676
Figure 1. Increase of Dehalogenimonas 16S rRNA gene copy numbers in Besòs River
677
cultures after consuming different doses of 1,2-DCP. Panel A: Consumption of 1,2-DCP
678
over time. The culture received several additions of 1,2-DCP, as indicated by the
679
arrows. Panel B: Dehalogenimonas 16S rRNA gene copies per mL of DNA in the 1,2-
680
DCP amended cultures. Error bars represent the standard deviation of copy numbers
681
measured in duplicate experiments for each point injected in triplicate.
682 683
Figure 2. Carbon isotopic composition of 1,2-DCP (circles) in methanogenic (solid
684
symbols) and non-methanogenic enrichment cultures containing 25 mM BES (open
685
symbols) during 1,2-DCP dechlorination. In non-methanogenic enrichment cultures,
686
carbon isotopic composition of propene was measured (stars) and values were corrected
687
to represent the generated propene (triangles) following equation 6 taking into
688
consideration the initial transfer of residual propene with the inoculum (see text). The
689
dashed line indicates the expected carbon isotopic mass balance which corresponds to
690
the initial 1,2-DCP composition (average value of -29.8 ± 0.3‰, n =11). The error bars
691
showing the one standard deviation (1σ) for duplicate measurements are smaller than
692
the symbols.
693 694
Figure 3. Double logarithmic plot according to the Rayleigh equation of the carbon
695
isotope ratio versus the residual concentration of 1,2-DCP during dechlorination by
696
methanogenic (solid symbols) and non-methanogenic enrichment cultures containing 25
697
mM BES (open symbols). The solid line corresponds to a linear regression model for
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total combined data (check Table 1 for more details) and gray dashed lines to its
699
associated 95% confidential intervals. Data points show their related error bars.
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FIGURE 1
A
1,2-DCP (µmol)
200 150 100 50
16S rRNA gene copies mL-1
0 7e+8
B
6e+8 5e+8 4e+8 3e+8 2e+8 1e+8 0 0
701
5
10
15
20
25
30
Time (d)
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FIGURE 2
703 704 705 20 10
δ13C [‰VPDB]
0 -10 -20 -30 -40 -50 0.0
0.2
0.4 0.6 0.8 Degraded fraction of 1,2-DCP
1.0
706
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FIGURE 3
708 0.05
ln(Rt/R0)
0.04
0.03
0.02
0.01
0.00 -3.5
-2.5
-1.5 ln(Ct/C0)
-0.5
0.5
709
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TABLE LEGENDS
711
Table 1. Carbon Isotope Fractionation (εCbulk) with 95% confidence intervals (95% CI) and calculated AKIE values assuming either stepwise or
712
concerted reductive dechlorination of 1,2-DCP. AKIE valuec Experiment
Suspected degrader
ɛCbulk (‰)
Na
R2
Db (%)
Non-methanogenic culture RC
Dehalococcoides
-10.8 ± 0.9
7
>0.96
>90
1.033 ± 0.003 1.016 ± 0.001
[13]
Non-methanogenic culture KS
Dehalococcoides
-11.3 ± 0.8
7
>0.96
>90
1.033 ± 0.003 1.017 ± 0.001
[13]
Methanogenic culture BR
Dehalogenimonas
-15.3 ± 0.7
12
0.996
94
1.046 ± 0.002 1.023 ± 0.001
This study
Non-methanogenic culture BR
Dehalogenimonas
-13.7 ± 2.0
8
0.98
77
1.042 ± 0.007 1.021 ± 0.003
This study
BR total combined data
Dehalogenimonas
-15.0 ± 0.7
20
0.991
94
1.045 ± 0.002 1.023 ± 0.001
This study
Stepwise
Concerted
Reference
713
a
714
b
715
c
716
carbon atoms located at the reactive site and z is the number of indistinguishable reactive sites, correcting the effects of intramolecular isotopic
717
competition. For 1,2-DCP, n =3 and the (x,z) considered for stepwise (1,1) and for concerted (2,1).
N: number of data points analyzed in duplicate. D%: maximum percentage of 1,2-DCP degradation which could be analyzed by GC-IRMS.
AKIE values were calculated according to reference [10] being n the number of carbon atoms in the molecule of which x is the number of
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