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Oneidensis MR-1 Produces: Cometabolism of CR (VI) by Shewanella Cell-Associated Reduced Chromium and Inhibits Growth
Oneidensis MR-1 Produces: Cometabolism of CR (VI) by Shewanella Cell-Associated Reduced Chromium and Inhibits Growth
Abstract: Microbial reduction is a promising strategy for denitrifying cells exposed to Cr(VI) showed reduced
chromium remediation, but the effects of competing chromium precipitates both extracellularly on the cell
electron acceptors are still poorly understood. We inves- surface and, for the first time, as electron-dense round
tigated chromate (Cr(VI)) reduction in batch cultures of globules inside cells. © 2003 Wiley Periodicals, Inc. Biotech-
Shewanella oneidensis MR-1 under aerobic and denitri- nol Bioeng 83: 627–637, 2003.
fying conditions and in the absence of an additional elec- Keywords: Shewanella oneidensis MR-1; chromate; re-
tron acceptor. Growth and Cr(VI) removal patterns sug- duction; denitrification; inhibition
gested a cometabolic reduction; in the absence of nitrate
or oxygen, MR-1 reduced Cr(VI), but without any increase
in viable cell counts and rates gradually decreased when
INTRODUCTION
cells were respiked. Only a small fraction (1.6%) of the
electrons from lactate were transferred to Cr(VI). The
48-h transformation capacity (Tc) was 0.78 mg (15 Hexavalent chromium [Cr(VI)] is an Environmental Protec-
µmoles) Cr(VI) reduced ⭈ [mg protein]−1 for high levels of tion Agency (EPA) priority pollutant and a known carcino-
Cr(VI) added as a single spike. For low levels of Cr(VI) gen. Due to its widespread industrial use, it is often found in
added sequentially, Tc increased to 3.33 mg (64 µmoles) contaminated groundwater. In order to achieve levels of
Cr(VI) reduced ⭈ [mg protein]−1, indicating that it is lim-
ited by toxicity at higher concentrations. During denitri-
chromium below the EPA maximum contaminant level (100
fication and aerobic growth, MR-1 reduced Cr(VI), with g/L), remediation strategies focus on the reduction of
much faster rates under denitrifying conditions. Cr(VI) Cr(VI) to insoluble trivalent forms, which are relatively
had no effect on nitrate reduction at 6 µM, was strongly stable and nontoxic. The only compounds able to oxidize
inhibitory at 45 µM, and stopped nitrate reduction above trivalent chromium at any appreciable rate are manganese
200 µM. Cr(VI) had no effect on aerobic growth at 60 µM,
but severely inhibited growth above 150 µM. A factor
oxides (Eary and Rai, 1987). Bioremediation may be effec-
that likely plays a role in Cr(VI) toxicity is intracellular tive for the removal of Cr(VI) from groundwater, as many
reduced chromium. Transmission electron microscopy aerobic and anaerobic microorganisms reduce Cr(VI) to
(TEM) and electron energy loss spectroscopy (EELS) of Cr(III) while utilizing a wide range of electron donors
(Bopp and Ehrlich, 1988; Ishibashi et al., 1990; Shen and
Wang, 1993; Rege et al., 1997; Tebo and Obraztsova, 1998;
Francis et al., 2000; Myers et al., 2000). However, there are
Correspondence to: Craig S. Criddle
Contract grant sponsor: the National Institute of Environmental Health
few studies that compare the kinetics of Cr(VI) reduction by
Sciences (NIEHS) Superfund Basic Research Program bacteria under different electron-accepting conditions or
Contract grant numbers: ES04911 (to the Institute for Environmental that study the effects of Cr(VI) on the reduction of other
Toxicology at Michigan State University), ES10337 to the University of electron acceptors.
California San Diego) Shewanella oneidensis MR-1 (formerly Shewanella pu-
Contract grant sponsor: the National Science Foundation Graduate Fel-
lowship Program (to SM)
trefaciens MR-1) is a facultative Gram-negative bacterium
Contract grant sponsor: the Swiss National Science Foundation Post whose respiratory versatility has prompted interest in its use
Graduate Fellowship (to RBL). in bioremediation. A nonfermenting bacterium, MR-1 can
628 BIOTECHNOLOGY AND BIOENGINEERING, VOL. 83, NO. 6, SEPTEMBER 20, 2003
soluble Cr(VI) and OD600. In addition, 2-mL samples were 4°C, followed by three 5-min changes of absolute ethanol at
centrifuged and the pellets stored at –20°C for subsequent room temperature. The cells were then infiltrated in a 1:1
total cellular protein analysis. mixture of absolute ethanol and Dow Epoxy resin (DER) for
1 h and left overnight in 100% resin. The cells were em-
bedded in DER and cured for 24 h at 60°C. The blocks were
Analytical Methods
thin-sectioned at 120–150 nm using a Leica Ultracut UCT
Soluble Cr(VI) was determined colorimetrically using 1,5- ultramicrotome. Sections were either left unstained or
diphenyl-carbazide in a sulfuric acid solution (pH 2) (San- stained with lead for less than 1 min.
dell, 1959). Samples were filtered with 0.2 m filters prior The sections were examined by a JEOL 4000× transmis-
to analysis. Absorbance was measured at 540 nm using a sion electron microscope (TEM) operated at 397 kV. EELS
Uvikon XL Spectrophotometer (Bio-Tek Instruments). To- spectroscopy is based on the energy loss experienced by a
tal soluble Cr was measured using a TJA IRIS Advantage/ TEM beam electron that ionizes an atom as it is transmitted
1000 Radial ICAP Spectrometer with a solid state CID De- through a thin section. The energy loss associated with the
tector. Nitrate and nitrite were measured using ion chroma- ionization of inner shell electrons is element-specific. Thus,
tography with a LC 20 ion chromatograph (Dionex, elemental composition can be derived from analyzing the
Sunnyvale, CA) equipped with CD 25 detector and an Ion- energy loss of electrons. For Cr, the ionization occurs at L2
Pac AS11-HC (4 mm) column (Dionex) using a sodium and L3 shells, thus producing a spectrum with two peaks.
hydroxide buffer (25 mM NaOH) at a flow rate of 1.5 The peaks correspond to an abrupt increase in electron en-
ml/min. Lactate and acetate were determined using ion ergy loss immediately above the threshold energy of ion-
chromatography with a 1 mM NaOH buffer. Protein was ization of an inner shell electron. For transition metals, the
measured using the Bradford assay (Sapan et al., 1999). valence of the element will affect peak position and the ratio
Viable cell numbers were determined by colony counts on of the area under the L2 and L3 peaks (for Cr). Thus, peak
LB medium. position and the peak area ratio of an element are used as
fingerprints for a valence state based on the spectra of va-
lence standards. Additionally, by selecting electrons with a
Reaction Kinetics
specific energy loss the distribution of the corresponding
Kinetics were described with a saturation kinetics expres- element in the specimen can be visualized (Elemental Map-
sion: ping). Detailed reviews of the EELS technique are available
(Gubbens and Krivanek, 1993; Egerton, 1996).
−dCr(VI)/dt ⳱ qmax[Cr(VI)/(K + Cr(VI)]*X
The electron energy loss spectroscopy (EELS) spectra
where dCr(VI)/dt ⳱ Cr(VI) reduction of rate [moles and the energy-filtered images were acquired with a Gatan
Cr(VI) reduced/L-h]; qmax ⳱ maximum specific Cr(VI) GIF200 charge couple device (CCD) camera and processed
reduction rate [moles Cr(VI) reduced/mg biomass (pro- by DigitalMicrograph v. 3.4 software. The spectra and fil-
tein)-h]; K ⳱ half-saturation coefficient [moles Cr(VI)/ tered images were corrected for dark current and channel-
L]; X ⳱ biomass concentration [mg biomass (as protein)/ to-channel gain variation of the CCD camera. EELS spectra
L]; Cr(VI) ⳱ Cr(VI) concentration [moles/L]. Kinetic pa- were obtained in the imaging mode of the TEM and in the
rameters were obtained using a nonlinear least-squares fit of spectroscopy mode of the GIF system with an energy dis-
the specific rate data using Micromath’s software program persion of 0.1 eV/channel. The collection angle was 2 ⳱
The Scientist. 100 mrad. The chromium elemental maps were collected
using the three-window method with pre-edges at 545 and
560 eV and a post-edge at 580 eV with a slit width of 20 eV.
TEM/EELS
EELS spectra were collected for the following standards:
MR-1 cells were grown aerobically overnight on LB liquid sodium chromate, Cr(III) oxide, and Cr(III)Cl3. The stan-
medium, pelleted, and washed in growth buffer three times. dards (in powder form) were placed on a carbon-coated Cu
The washed cells were used to inoculate 180 mL serum grid and placed directly in the sample holder. The sample
bottles containing 5 mM nitrate and 10 mM lactate in the holder was then placed under vacuum. EELS spectra were
minimal medium previously described. After 16 h (OD600 analyzed to determine the ratio of the area under the L3 and
⳱ 0.6), sodium chromate was added to a final concentration L2 chromium peaks. First, the background subtraction fea-
of 0.2 mM. After 24 h, Cr(VI) was completely reduced. The ture of DigitalMicrograph was used to remove the back-
cells were centrifuged and the supernatant discarded. A se- ground. The surface area under each peak was determined
ries of pelleting and resuspension steps followed. Bacterial by integration of a 3 eV region around the top of the peak
cells were fixed in a mixture consisting of 2% acrolein, 2% (a 5eV region gives the same result) using a modified ver-
glutaraldehyde, and 2% paraformaldehyde in HEPES (pH sion of the Flat Two Step method (Daulton et al., 2002) and
7.5) buffer for 30 min at room temperature. Cells were the ratio of the two peaks was calculated.
washed three times in buffer and three times in double- TEM images of stained sections were also obtained by a
distilled water, each for 3 min. The cells were dehydrated by JEOL 2000FX microscope operating at 80 kV and equipped
an ethanol series of 70%, 90%, and 100% for 5 min each at with a Teitz TemCam F224 2K × 2K CCD camera.
Figure 1. Shewanella oneidensis MR-1 reduces Cr(VI) in the absence of other electron acceptors, but does not grow on Cr(VI). Where error bars are
shown, values are the average of duplicates and error bars represent the range. 50 M Cr(VI) was added at day 2 and 5. (⽧), MR-1 + lactate + Cr(VI);
(䉭), MR-1 + Cr(VI); (䊉), Cr(VI) + lactate; (䊊), autoclaved MR-1 + lactate + Cr(VI); and (*), viable cell count for MR-1 + lactate + Cr(VI).
630 BIOTECHNOLOGY AND BIOENGINEERING, VOL. 83, NO. 6, SEPTEMBER 20, 2003
Figure 2. MR-1 reduces nitrate and nitrite and oxidizes lactate to acetate in the absence of Cr(VI) (A) and with 6 M Cr(VI) (B). 45 M Cr(VI) (C)
severely inhibits the rate of nitrate and nitrite reduction and lactate oxidation. Growth is inhibited by 45 M Cr(VI) or the absence of lactate (D). Cr(VI)
additions were made at 3 h. A–C: (䊉), nitrate; (䊊), nitrite; (⽧), lactate; (䊐), acetate; (⌬), Cr(VI). D: (䊏), no Cr(VI); (䉭), 6 M Cr(VI); (−), 45 M Cr(VI);
(*), no lactate.
Additional experiments elucidated the effect of varying 2, range given) was obtained at 7 M Cr(VI); this value
Cr(VI) concentrations on specific rates of nitrate reduction. increased to 0.016 ± 0.00003 (n ⳱ 3) at 40–50 M Cr(VI).
Cultures were spiked with 2 mM nitrate and allowed to A larger fraction of electrons is transferred to Cr(VI) at
grow for ∼30 min before being spiked with Cr(VI). Specific higher initial Cr(VI) concentrations where Cr(VI) reduction
rates of nitrate reduction were computed from data points rates are faster. To ensure that the hydrogen present in the
taken in the first 2 h following addition of Cr(VI). Figure 3 headspace (taken from the anaerobic chamber) did not in-
displays the specific rate of nitrate reduction as a function of fluence calculations, experiments were repeated using inert
initial Cr(VI) concentration. Initial rates of nitrate reduction gases in the headspace (He and N2/CO2). There was no
decreased with increasing levels of Cr(VI). Above 190 M statistical difference in the values.
Cr(VI), nitrate reduction stopped.
An electron balance was determined for nitrate and chro-
mate reduction by MR-1. Using the following half reac-
tions, the changes in lactate, nitrate, and Cr(VI) concentra-
tion could be expressed in terms of moles of electron
equivalents:
632 BIOTECHNOLOGY AND BIOENGINEERING, VOL. 83, NO. 6, SEPTEMBER 20, 2003
Table I. 48-h Cr(VI) transformation capacity of S. oneidensis MR-1 aerobic cultures exposed to 150, 200, and 400 M Cr(VI);
under three experimental conditions following a single spike of Cr(VI) 60 M Cr(VI) had little effect (Fig. 4b). A lag time of ∼2 h
ranging from 200–500 M.
was observed before inhibition of growth occurred.
Transformation
capacity ± one
standard deviation
Transformation Capacity
Experimental [mg Cr(VI) When spiked with concentrations of Cr(VI) above 150 M,
condition reduced/mg protein]
MR-1 gradually lost its ability to reduce Cr(VI) with time
Resting cells with Cr(VI) as only e- acceptor 0.78 ± 0.31 (n ⳱ 6) under both anaerobic and aerobic (Fig. 4) conditions. This
In the presence of nitrate 0.54 ± 0.14 (n ⳱ 9) may indicate a finite reduction capacity per cell. The con-
Aerobic conditions 0.08 ± 0.02 (n ⳱ 6)
cept of transformation capacity (Tc) was first introduced by
Alvarez-Cohen and McCarty (1991), who defined it, for
resting cells, as the mass of nongrowth substrate trans-
These results demonstrate the simultaneous reduction of formed per unit of biomass. In this work, Tc was estimated
Cr(VI) and nitrate and the inhibitory effect of Cr(VI) on as the mass of Cr(VI) reduced per unit biomass present (mg
denitrification. The low fraction of electrons directed to protein) after 48 h. A duration of 48 h was chosen because
Cr(VI) suggests secondary utilization or a cometabolic pro- the rate of Cr(VI) reduction typically approached zero by
cess. this time. The mass of Cr(VI) reduced in controls without
cells was subtracted from the overall mass transformed. We
used data from resting cultures of MR-1 and from those
Cr(VI) Reduction During Aerobic Growth
grown on nitrate and oxygen to compute transformation
Studies were performed to study Cr(VI) reduction during capacities. These values were significantly different for
aerobic growth. Cr(VI) was added in the early logarithmic aerobic and anaerobic conditions and are shown in Table I.
phase of growth at varying concentrations. Approximately The rate of Cr(VI) reduction decreased gradually for rest-
100 M Cr(VI) was reduced when lactate was present as ing cells receiving sequential spikes of 50–75 M Cr(VI)
electron donor (Fig. 4), irrespective of the amount of Cr(VI) (Fig. 1). However, sequential spikes of lower levels of
added. In abiotic controls with lactate and Cr(VI), ∼23 M Cr(VI) allowed for a larger transformation capacity over a
was reduced in 20 h (data not shown). As discussed earlier, longer duration than single spikes of higher Cr(VI) concen-
this reduction was likely due to abiotic reduction of Cr(VI) trations. In resting anaerobic cultures, up to 3.5 mg (67 M)
by medium components. Slightly more Cr(VI) was reduced Cr(VI) ⭈ [mg protein]−1 was reduced with sequential spikes
in controls without electron donor (27 M), as seen previ- of ∼75 M Cr(VI) over the course of 30 days (data not
ously for anaerobic resting cells. Growth was inhibited in shown), as opposed to 0.78 mg Cr(VI) ⭈ [mg protein]−1 for
Figure 5. The rate of Cr(VI) reduction by MR-1 cells is first order with respect to biomass concentration. Cells were resting anaerobically with [Cr(VI)]
⳱ 250 M and no other electron acceptors. Values are the average of triplicates ± 1 SD, (⽧), dCr(VI)/dt.
cells exposed to a single spike of Cr(VI) at higher concen- order of magnitude larger than under aerobic conditions.
trations. This suggests that transformation capacity is lim- However, qmax for anaerobic cells with and without nitrate
ited by Cr(VI) toxicity at higher concentrations. The limited were not statistically different, in contrast to results reported
transformation capacity per unit biomass compounded by by Viamajala et al. (2002). The contrasting results may be
the inhibitory effect of Cr(VI) on growth could pose a chal- explained by differences in experimental conditions such as
lenge for chromate bioremediation. growth phase of cells and time elapsed during rate measure-
ments, as well as the fact that our parameters were obtained
through the modeling of data taken at a wide range of
Reaction Kinetics
Cr(VI) concentrations.
Studies were performed to evaluate reaction kinetics. The For all three electron accepting conditions, the values for
Cr(VI) reduction rate was first order with respect to biomass K (29–88 M) are much larger than the regulatory standard
(Fig. 5). Rate experiments were carried out under the three of 1.9 M. This indicates that first-order kinetics would
electron-acceptor conditions studied. Cr(VI) was added at likely limit the rates of Cr(VI) reduction and rates will de-
10–400 M to batch cultures of MR-1. Data points taken in crease as concentrations fall. Since initial rates of Cr(VI)
the first 0–2 h following Cr(VI) addition were used to com- reduction are used in the computation of qmax and K, we did
pute initial rates of Cr(VI) reduction, which were then nor- not consider the effects of transformation capacity.
malized to the biomass present during the same time period.
As shown in Figure 6, the kinetic data followed a saturation
TEM/EELS
kinetics pattern, with specific rates approaching a maxi-
mum, qmax, at higher concentrations. Table II provides a TEM images of cells in the presence of chromium showed
summary of the kinetic parameters for all three electron- electron-dense precipitates both around and inside cells
acceptor conditions; qmax under anaerobic conditions was an (Fig. 7A). The majority of cells contained intracellular pre-
Table II. Kinetic parameters for S. oneidensis MR-1 under three electron-accepting conditions.
Values are based on a nonlinear least squares fit of the specific rate data using saturation kinetics (see text). Experiments were performed in triplicate
and standard deviations are indicated.
634 BIOTECHNOLOGY AND BIOENGINEERING, VOL. 83, NO. 6, SEPTEMBER 20, 2003
duced chromium within cells. In addition, there was a sig-
nificant amount of intracellular chromium that was not as-
sociated with the globules but diffused throughout the cy-
toplasm. A study of the peak position and the peak ratio
relative to the oxidation state showed that chromium asso-
ciated with cells (both intracellularly and extracellularly)
does not correspond to Cr(VI) (Fig. 8). It appears to be most
closely related to Cr(III) but does not overlap either of the
two Cr(III) forms probed (chloride and oxide). The structure
and position of the L2 and L3 chromium peaks depend on
the local electronic structure of the atom. Both the oxidation
state and the chemical environment of the chromium atoms
determine the position and the ratio of the two peaks. There-
fore, it is likely that the chromium in and around the cells is
in a reduced form (most likely Cr(III)) but the definitive
chemical form is unknown. These results strongly suggest
that Cr(VI) is transformed inside cells.
A recent EELS study examined Cr(VI) reduction by
MR-1 (Daulton et al., 2002). They showed chromium in a
reduced oxidation state (probably Cr(III)) surrounding the
cells, but did not identify intracellular chromium. Their con-
ditions differed from this study in that the cells were ex-
posed to 0.1 mM Cr(VI) as the sole terminal electron ac-
ceptor for 30 days. In our 2-day experiments, Cr(VI) was
added at 0.2 mM to cells grown on nitrate as the terminal
electron acceptor. The absence of intracellular chromium in
their work is not necessarily incompatible with our results.
Their study did not include an elemental map of the cell thin
section. It is conceivable that there was chromium present
intracellularly but did not form the distinctive round glob-
ules that we found in our system due to differences in ex-
perimental conditions. Other researchers have observed
similar round bodies of reduced selenium in the cytoplasm
of Ralstonia metallidurans CH34 (Roux et al., 2001).
There are widespread reports of the intracellular interac-
tion of Cr(III) with DNA (Gulanowski et al., 1992; Zhitko-
vich et al., 1996). Cr(III) has been reported to crosslink the
phosphate backbone of DNA with peptides and amino acids
such as cysteine and histidine (Zhitkovich et al., 1996). We
postulate that the round globules present in a large number
of the cells is due to this cross-linking, causing Cr(III) to be
Figure 7. A: Transmission electron microscopy (TEM) image of S.
bound to phosphate and amino groups. This might explain
oneidensis MR-1 after reduction of 0.2 mM Cr(VI). Cells were grown on
nitrate. Sections with stained with lead. Bar ⳱ 1 m. B: Electron energy the imperfect match with the exclusively inorganic stan-
loss spectroscopy (EELS) was used to create an elemental map of chro- dards used to characterize the peak position and L3/L2 peak
mium (red) overlaid on a zero energy loss filtered image of an MR-1 cell area ratio. Cr(III) interaction with DNA is known to in-
(section stained with lead). The electron-dense precipitates both inside and crease the rate of DNA polymerase bypass of DNA lesions
outside the cell are reduced chromium, including the electron-dense glob-
resulting in an increase in spontaneous mutagenesis (Snow,
ules in the cytoplasm. Bar ⳱ 25 nm.
1994). The observed inhibitory effect of Cr(VI) on the
growth and metabolism of MR-1 may be due to the delete-
cipitates in the form of round globules. Electron-dense pre- rious interaction of intracellular Cr(III) with DNA.
cipitates were not observed in cells that were not exposed to
chromium (not shown). An elemental map of chromium
CONCLUSIONS
overlaid on a zero-energy-loss filtered image of an MR-1
cell (stained with lead) showed that the electron-dense pre- Many electron acceptors are present in contaminated sys-
cipitates outside the cell and the large electron-dense glob- tems and often vary spatially and with time. That MR-1 is
ules inside the cells were chromium (Fig. 7B). To our able to reduce Cr(VI) in environments containing oxygen or
knowledge, this is the first report of round globules of re- nitrate augers well for its use in bioaugmentation applica-
tions. Bacteria often preferentially utilize more energeti- precipitates both within and surrounding cells, including
cally favorable electron acceptors. For example, in the pres- intracellular reduced chromium globules, that may contrib-
ence of nitrate, reduction of Mn(IV), thiosulfate, and Fe(III) ute to the inhibitory effects of chromium.
in Shewanella putrefaciens 200 was inhibited, indicating
that nitrate was the preferred electron acceptor for anaerobic We thank James Bouwer from the National Center for Micros-
respiration (DiChristina, 1992). Although oxygen and ni- copy and Imaging Research for help with the Gatan Imaging
Filter. We also thank Jizhong Zhou for supplying the MR-1 strain
trate have half-reaction reduction potentials that are higher
used in this study, and Alfred Spormann and Weimin Wu for
or comparable (respectively) to Cr(VI), MR-1 is able to helpful suggestions on the manuscript.
reduce Cr(VI) while reducing both of these electron accep-
tors. These results suggest that in bioremediation applica-
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