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Applied and Environmental Microbiology, September 2001, p. 3785-3794, Vol. 67, No. 9
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.9.3785-3794.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Identification and Characterization of Bacteria in
a Selenium-Contaminated Hypersaline Evaporation Pond
M. P.
de
Souza,1
A.
Amini,1
M. A.
Dojka,1
I. J.
Pickering,2
S. C.
Dawson,1
N. R.
Pace,
and
N.
Terry1,*
Department of Plant and Microbial Biology, University of
California, Berkeley, California 94720-3102,1
and Stanford Synchrotron Radiation Laboratory, Stanford Linear
Accelerator Center, Menlo Park, California
94025-70152
Received 16 March 2001/Accepted 12 June 2001
 |
ABSTRACT |
Solar evaporation ponds are commonly used to reduce the volume of
seleniferous agricultural drainage water in the San Joaquin Valley,
Calif. These hypersaline ponds pose an environmental health hazard
because they are heavily contaminated with selenium (Se), mainly in the
form of selenate. Se in the ponds may be removed by microbial Se
volatilization, a bioremediation process whereby toxic, bioavailable
selenate is converted to relatively nontoxic dimethylselenide gas. In
order to identify microbes that may be used for Se bioremediation, a
16S ribosomal DNA phylogenetic analysis of an aerobic hypersaline pond
in the San Joaquin Valley showed that a previously unaffiliated group
of uncultured bacteria (belonging to the order
Cytophagales) was dominant, followed by a group
of cultured
-Proteobacteria which was closely related
to Halomonas species. Se K-edge X-ray absorption
spectroscopy of selenate-treated bacterial isolates showed that they
accumulated a mixture of predominantly selenate and a
selenomethionine-like species, consistent with the idea that selenate
was assimilated via the S assimilation pathway. One of these bacterial
isolates (Halomonas-like strain MPD-51) was the best
candidate for the bioremediation of hypersaline evaporation ponds
contaminated with high Se concentrations because it tolerated 2 M
selenate and 32.5% NaCl, grew rapidly in media containing selenate,
and accumulated and volatilized Se at high rates (1.65 µg of Se g of
protein
1 h
1), compared to other cultured
bacterial isolates.
 |
INTRODUCTION |
The soils in the Central
Valley of California and other western states are derived from shale
rocks that naturally contain high levels of Se, B, As, V, Sr, and other
potentially toxic elements (12). When the fields are
irrigated, large volumes of agricultural drainage water are produced
that contain high levels of Se, mainly in the form of selenate
(25). Solar evaporation ponds are commonly used to reduce
the volume of selenate-contaminated agricultural drainage water
(29). Agricultural drainage water is pumped into the ponds
and allowed to evaporate, leaving patches of salt and brine containing
high concentrations of Se, which pose a threat to wildlife via
bioaccumulation and biomagnification in the food chain
(30). For example, when Se-contaminated agricultural
drainage water was released to the Kesterson reservoir, fish and birds accumulated very high concentrations of Se that resulted in
reproductive and developmental deformities and even death
(28, 31).
In spite of the ecotoxicological effects of Se and other elements that
accumulate to high levels, solar evaporation ponds are still being used
in California and other western states to reduce the large volumes of
Se-contaminated drainage water (29). An alternative
approach to reducing the volume of Se-contaminated drainage water is to
use integrated on-farm drainage management (IFDM); i.e., drainage water
is reduced in volume by being recycled through a successive series of
crops, each of which is more salt tolerant than the preceding crop. The
small amount of drainage water that remains after recycling through the
different crops is ultimately collected in a plastic-lined solar
evaporation pond. The IFDM approach has been investigated at Red Rock
Ranch in Five Points, Calif. (6).
The microbial composition of this terminal solar evaporation pond is of
considerable interest with respect to Se bioremediation. This is
because the microbes are able to survive the extremely high levels of
salt, Se, and other potentially toxic elements (substrates that totally
exclude the growth of higher plants) and because the microbes have the
ability to remove the Se through volatilization to the atmosphere
(11). There are several ways in which microbes from the
solar evaporation pond are of interest with respect to the remediation
of Se-contaminated drainage water. First, they could be used for the
bioaugmentation of evaporation ponds to increase Se removal by
increasing the rate of Se volatilization from the ponds. Second, they
represent a reservoir of microbes that could be used in a bioreactor
especially developed for the remediation of agricultural drainage
water. Third, they represent a reservoir of genes encoding enzymes that
are able to facilitate tolerance to extremely high concentrations of Se
and salt, possibly by allowing the uptake and assimilation of Se, for
example, to volatile forms, so that Se may be dissipated harmlessly.
Such genes could be used, for example, for incorporation into plants for the phytoremediation of Se.
Biological volatilization of inorganic forms of Se (selenate and
selenite) to gaseous forms can be carried out by plants and microbes
(see references 11 and 35 for reviews) and is
an especially important pathway of Se removal. Selenium-volatilizing microalgae and bacteria have been isolated from Se-contaminated ponds
containing agricultural drainage water (10, 26). The overwhelming advantage of Se volatilization is that it physically removes Se from the site, minimizing the ecotoxic effects of Se. Furthermore, dimethylselenide, the predominant form of volatile Se
produced by microbes in solar evaporation ponds (36), is 500 to 700 times less toxic than selenate (38). Terry and
Lin (34) made field measurements of the rate of Se
volatilization by different components of the IFDM system at Red Rock
Ranch. From their measurements of Se volatilization from the solar
evaporation pond, they estimated that 6% of the Se entering the pond
was removed via volatilization in 1 year (34). It would be
tremendously beneficial to find ways to significantly enhance Se
removal above this 6% level.
A major factor influencing Se volatilization in evaporation ponds is
microbial community composition (in addition to other factors, such as
the levels of nutrients and sulfate, oxygen tension, temperature, pH,
Se forms, and concentration) (11). The goal of the present
work was to determine the role of microbial community composition as a
prime factor controlling Se volatilization in a solar evaporation pond.
This was achieved by means of a 16S ribosomal DNA (rDNA) phylogenetic
analysis that was carried out on salt from the Red Rock Ranch
evaporation pond. The specific objectives were to (i) identify the
microbial populations present in the solar evaporation pond at Red Rock
Ranch and (ii) determine which culturable microbes have superior
capacities for Se assimilation and volatilization and therefore
bioremediation. To this end, the culturable microbes were tested with
respect to their efficiency in accumulating, assimilating, and
volatilizing Se and for their tolerance to high levels of Se and salt.
Using Se K-edge X-ray absorption spectroscopy (XAS), the chemical forms
of Se accumulated by the bacteria were identified so as to
ascertain their biochemical pathway of Se assimilation.
 |
MATERIALS AND METHODS |
Site description.
The solar evaporation pond which was used
as a sampling site in the present study was the terminal step of an
IFDM system at Red Rock Ranch (6, 34). The IFDM system
consists of several cells in series. The drainage water from 192 ha of
salt-sensitive crops (Alfalfa) is used to irrigate 52 ha of
salt-tolerant crops (Brassica napus), whose drainage water
is supplied to 5 ha of trees (Eucalyptus). The saline
drainage water from the trees is used to irrigate 1.85 ha of halophytes
(Salicornia bigelovii, Atriplex patula,
Distichilis spicata, and Spartina gracilis). The
hypersaline drainage water from the halophyte cell is sprayed into an
unvegetated, plastic-lined 0.73-ha solar evaporation pond. A damp salt
sample was collected from the solar evaporation pond in March 1997. At
the time of sample collection, the electrical conductivity (EC) of the
brine in the pond was 75 mS cm
1, the pH was
8.5, and the Se concentration was 5 mg liter
1
(34).
Isolation of bacteria from the solar evaporation pond.
The
sample of solar evaporation pond salt was maintained at 4°C
until it was brought back to the laboratory. The sample was stirred to
mix it, and 0.5 g of the sample was immediately frozen at
80°C
for DNA extraction. Another 15 g of the mixed salt sample was
added to 100 ml of an enrichment medium and maintained for 1 week in
the dark on a shaker (100 rpm) at room temperature; the enrichment
medium contained (per liter) 500 ml of Hoagland's solution
(15), 1 ml of vitamin solution (7), 0.1 g of yeast extract, and 5 mM sodium acetate. The pH of the medium was
8.5. Aliquots (50 µl) of the enrichment culture were spread on plates of isolation medium, which was similar to enrichment medium but also
contained 70 µM (5.6 mg of Se liter
1) sodium
selenate (Sigma), 5 g of NaCl liter
1, and
15 g of Difco agar liter
1.
DNA isolation and cloning of 16S rDNA.
In order to determine
the identities of both unculturable and culturable microbes in the
solar evaporation pond, DNA was isolated by bead beating of a frozen
salt sample and then by using the phenol-chloroform procedure described
in detail for the extraction of DNA from soil (9). A smear
of DNA was observed after electrophoresis on a 1% polyacrylamide gel.
This smear was cut out from the gel, and the DNA was cleaned using a
Geneclean II kit (Bio 101, Inc., La Jolla, Calif.). Seven 10-fold
dilutions of the DNA were made with water and used as templates for
PCRs with small-subunit (SSU) rDNA primers 1492R (5'-GGT
TAC CTT GTT ACG ACT T-3') and 533F (5'-GTG CCA GCM GCC GCG
GTA A-3') and the PCR protocol described earlier
(9). A PCR product was obtained for the DNA at a 1:100 dilution. This product was cloned using a TA cloning kit as described in the kit instructions (Invitrogen). Clones were checked for the
presence of the insert by preparing plasmids with a Qiagen kit,
digesting the plasmids with EcoRI, and checking for the
presence of the insert by electrophoresis on a 1% polyacrylamide gel.
Restriction fragment length polymorphism (RFLP) analysis of the 16S
rDNA clones was carried out to rapidly estimate the microbial diversity
in the solar evaporation pond. rDNA inserts from recombinant clones
were reamplified by PCR, after which 25 µl of PCR product was
digested overnight at 37°C with 1.5 U of each of the 4-base-specific restriction endonucleases MspI and HinPII in NEB2
buffer (New England Biolabs) at a final volume of 30 µL. Digested
fragments were separated by electrophoresis on a 2% agarose gel and
visualized by staining with ethidium bromide and UV illumination. RFLP
patterns were grouped visually, and representatives were selected for
DNA sequencing.
Sequencing of rDNA clones, phylogenetic analyses, and chimera
detection.
Plasmid templates from representative clones were
sequenced using an ABI 373 Stretch DNA sequencer (Dye-Terminator Cycle
Sequencing Ready Reaction FS kit; PE Applied Biosystems) according to
the manufacturer's instructions. Primers used for sequencing included vector primers and the 1492R and 533F SSU rDNA primers. Sequences were
compared to available databases by use of the BLAST (Basic Local
Alignment Search Tool) network service (1) to determine their approximate phylogenetic affiliations. Partial sequences were
compiled with AutoAssembler 2.1 (PE Applied Biosystems); compiled
sequences were aligned by use of the ARB database
(http://www.mikro.biologie.tu-muenchen.de). Chimeric sequences were
identified with the CHECK_CHIMERA program (20) and by
secondary-structure anomalies. Sequence alignments used for
phylogenetic inference were minimized by use of the Lane mask
(17) for bacterial data. The dendrogram was constructed by
use of the ARB database with evolutionary distance (neighbor-joining algorithms with Olsen correction). The robustness of inferred topologies was tested by bootstrap resampling of trees calculated with
evolutionary distance (version 4.0b2 of PAUP*; neighbor-joining algorithm with either Kimura two-parameter correction or
maximum-likelihood correction with an empirically determined gamma
distribution model of site-to-site rate variation and empirically
determined base frequencies) (33), parsimony (version
4.0b2 of PAUP*; heuristic search) (33), and maximum
likelihood (fast DNAml in the ARB database)
(http://www.mikro.biologie.tu-muenchen.de).
Measurements of bacterial growth rates, Se accumulation, and
volatilization.
Phylogenetically distinct bacterial strains were
characterized with regard to their growth in the presence of high Se
concentrations and their ability to take up and volatilize Se. Cells
were grown in sterile Nalgene beakers that contained 600 ml of sterile
isolation medium (minus the agar) and that were placed in airtight Se
volatilization chambers (8). Three replicate chambers were
used for each bacterial strain. The chambers were sterilized by
treating them with 20% bleach and washing them with sterile distilled
water. Volatile Se that was produced by the cultures was trapped in gas
washing bottles (Fisher), which contained 200 ml of alkaline peroxide (40 ml of 30% H2O2, 160 ml
of 0.05 M NaOH). Volatile Se was trapped by pulling a vacuum on the
chamber outlet, which resulted in sterile air being bubbled into the
culture via a 0.2-µm filter (Gelman) on the inlet to the chamber.
Samples (5 ml) of the alkaline peroxide trap solution were collected at
12 different time points during the course of bacterial growth. The
samples were heated at 92°C for 30 min in a water bath, 5 ml of
concentrated HCl was added, and the samples were heated again at 92°C
for 30 min. The Se content in these samples was determined by atomic
absorption hydride-generation spectroscopy (22). The rates
of Se volatilization (micrograms of Se gram of
protein
1 hour
1) were
calculated from the amount of Se volatilized during the last two time
points in the exponential phase of growth and normalized to the protein
content at the last time point in the exponential phase.
A 1-ml sample of culture solution was withdrawn from each of the
chambers during the first five time points to measure bacterial growth.
After the first five time points, there was enough bacterial growth to
measure Se bioaccumulation. Twenty-five milliliters of culture solution
was collected at each of the remaining seven time points to measure Se
bioaccumulation in addition to growth. Strain MPD-72 was the only
exception; for this strain, 25 ml of culture solution was collected for
Se analysis at the fourth time point as well as the remaining eight
time points. This exception was made because preliminary growth curves
showed that MPD-72 had a shorter lag phase than the other strains.
Growth was monitored by measuring the optical density at 600 nm and by
measuring the protein content of the culture. The bacterial cells in
0.5 ml of each culture were lysed using alkaline hydrolysis
(7), and their protein contents were measured using the
Bradford assay (Bio-Rad) in accordance with the manufacturer's instructions.
Se bioaccumulation in the bacterial cultures was measured as
follows. The 25-ml sample of each bacterial culture was centrifuged at
8,000 × g for 10 min. The pellets were washed with 10 ml of sterile saline (0.85% NaCl) and recentrifuged at 8,000 × g for 10 min. The washed pellets were digested overnight at
room temperature in 50-ml Pyrex digestion tubes with 1 ml of
concentrated nitric acid. Glass funnels were placed on the digestion
tubes, which were then heated in a digestion block (Tecator model 2040)
at 130°C for 5 h. The volume of the acid digests was brought to
10 ml with deionized water. One milliliter of these digests was heated with 1 ml of 30% hydrogen peroxide at 92°C for 30 min in a water bath, after which 5 ml of concentrated HCl was added and the samples were heated again at 92°C for 30 min. Atomic absorption spectroscopy was used to measure total Se in the acid digests (22). At
the end of the growth experiment, the remaining culture (~300 ml) was
centrifuged and washed as described above. Glycerol (100 µl) was
added to each of the washed pellets, which were then frozen at
80°C
for XAS analysis of the chemical forms of Se that accumulated in the
bacterial cells.
In a separate experiment, the bacterial strains were tested for
halotolerance and Se tolerance, based on their ability to grow in media
containing different concentrations of NaCl and selenate, respectively.
The cultures were grown aseptically in flasks containing 250 ml of
isolation medium (minus the agar). The flasks were placed on a shaker
at 150 rpm for 3 days at room temperature. The cultures were
centrifuged at 8,000 × g and washed with sterile
saline, and the pellets were resuspended in 5 ml of saline. These
cultures (25 µl) were used to inoculate culture tubes containing 5-ml
quantities of different batches of liquid medium to determine the
effect of 6 NaCl concentrations and 8 selenate concentrations on
bacterial growth. The medium for the NaCl experiment was the same as
isolation medium except that it contained 0, 0.1, 1, 5, 10, 15, 20, or
32.5% NaCl but did not contain any selenate or agar. Culture solutions
containing 5, 10, 15, and 20% NaCl culture solutions gave EC values of
79, 148, 296, and 422 mS cm
1,
respectively, when measured with a Checkmate EC meter (Corning). These values were obtained after the solutions were diluted 10- or
100-fold with deionized water. Solutions containing 25 or 32.5% NaCl
gave the same EC value as the 20% NaCl solution. The medium for the
selenate experiment was the same as isolation medium except that it
contained 5 g of NaCl liter
1; no sodium
selenate or 0.2 µM, 2 µM, 20 µM, 200 µM, 2 mM, 20 mM, 200 mM,
or 2 M sodium selenate; and no agar. For conversion of these molar
quantities into mass concentrations, 0.2 µM selenate is approximately
equivalent to 16 µg of Se liter
1. The
bacterial cultures were inoculated into triplicate tubes containing
each type of medium. All tubes were placed in a shaker maintained at
250 rpm for 1 week at room temperature. The absorbance of each culture
tube was measured at 600 nm as an indicator of growth.
Identification of bioaccumulated Se.
XAS was used to
determine the form of bioaccumulated Se in the frozen pellets of each
bacterial culture as described previously (37). XAS
analyses of all frozen samples were performed at the Stanford
Synchrotron Radiation Laboratory (SSRL) with Beam Line 4-3. A Si(220)
double-crystal monochromator was used with an upstream vertical
aperture of 1 mm, and harmonic rejection was achieved by detuning one
crystal by 50%. The electron energy was 3.0 GeV, with a current of 50 to 100 mA. Frozen samples were positioned at a 45° angle to the X-ray
beam and were maintained at 15 K in a liquid He cryostat. Se K-edge
X-ray absorption spectra were collected by monitoring the Se
K
fluorescence using a Canberra 13-element Ge detector in a series of replicate scans dependent on
trace element concentrations. Spectra were also collected for Se
references, i.e., 10 mM aqueous solutions of sodium selenate, sodium
selenite, and selenomethionine (SeMet) and solid red elemental selenium
(23), the latter being collected in transmission. All samples were calibrated against a hexagonal elemental Se reference foil, the spectrum of which was collected simultaneously with the data
in transmission and the first energy inflection of which was assumed to
be 12,658.0 eV. Data were collected using the XAS-Collect program
(13) and analyzed using the EXAFSPAK suite of programs (http://ssrl.slac.stanford.edu/exafspak.html). Quantitative analysis using an edge-fitting method was carried out according to the methods
of Pickering and coworkers (23) and Van Fleet-Stalder et
al. (37). The advantage of using XAS is that it determines the form of Se in vivo, without any need for chemical extraction of Se,
which may alter the form of Se in the cell. The production of elemental
Se was also evaluated by visually examining the cultures for orange
particles, which are characteristic of elemental Se produced via
bacterial dissimilatory selenate reduction (32).
Nucleotide sequence accession numbers.
The sequences of the
rDNA clones have GenBank accession numbers AF348707 to AF348733.
 |
RESULTS |
Based on the composition of the salt crystals from the Red Rock
Ranch evaporation pond, it seems clear that any microbes surviving in
the salt could withstand high concentrations of Se and salt (Table
1). The salt crystals contained a Se
concentration of 200 mg kg of dry weight
1 and
very high concentrations of other elements, especially sulfur, which
made up almost 25% of the salt. The Se concentration in the salt was
40-fold higher than that in the brine in the solar evaporation pond,
which had a Se concentration of ~5 mg liter
1
in March 1997, when salt samples were collected (34).
In order to identify evaporation pond microbes that would be superior
for Se bioremediation, the microbial community in the salt from the
solar evaporation pond was identified by sequencing clones of the
community rDNA. These clones were obtained from the total DNA extracted
from the salt. A phylogenetic analysis of 72 clones of 16S rDNA
identified members of the Bacteria; no members of the
Archaea were found (Fig. 1).
The most dominant group was a previously unaffiliated group of bacteria
placed in the order Cytophagales. This group had 30 clones
with similar sequence identities or RFLP patterns (Table
2) and 88% sequence identity to
Rhodothermus marinus. However, none of these bacteria could
be cultured. The second most dominant group consisted of Halomonas species placed in the class
-Proteobacteria; some of these bacteria could be cultured
(Table 2). Several additional clones were identified as members of
different bacterial groups, i.e.,
-Proteobacteria,
-Proteobacteria, low G+C-content gram-positive bacteria,
Actinobacteria, and Verrucomicrobiae.

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FIG. 1.
Evolutionary distance dendrogram of bacterial 16S rDNA
sequence types obtained from the selenium-contaminated solar
evaporation pond. Bacterial groups are listed outside the brackets.
Reference sequences were chosen with the ARB parsimony insertion tool
and database (http://www.mikro.biologie.tu-muenchen.de) and the BLAST
program (1). Branch points supported (bootstrap values of
>74%) by rate-corrected maximum-likelihood, parsimony, and distance
analyses are indicated by closed circles. Cultivated organisms are
indicated with asterisks.
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The physiology of Se assimilation and volatilization was studied with
six bacterial strains cultured from the hypersaline pond: three strains
closely related to Halomonas species (MPD-51, MPD-61, and
MPD-72) and strains related to Microbacterium saperdae (MPD-60), Bacillus firmus (MPD-67), and
"Agrobacterium sanguineum" (MPD-70). These six
cultured strains of bacteria were grown in a medium containing 5 mg of
selenate liter
1, a concentration similar to
that of the water in the solar evaporation pond at the time of sample
collection (34). The bacterial strains were studied with
respect to their growth, salt and Se tolerance, rate of Se
volatilization, and amount and chemical form of Se that they accumulated.
Two measures of growth, i.e., the turbidity of the culture and the
protein content of the bacteria, were used to determine the rate of
bacterial growth. Both indicators of growth showed that the strains
related to Halomonas (MPD-51, MPD-61, and MPD-72) and
M. saperdae (MPD-60) grew best in the liquid medium
containing selenate, whereas the strains related to "A.
sanguineum " (MPD-70) and B. firmus (MPD-67) grew
relatively poorly (Fig. 2). The growth curve based on the protein content of the bacterial cells paralleled the growth curve obtained from the turbidity measurements.

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FIG. 2.
Growth curves and protein contents of bacterial isolates
from the selenium-contaminated solar evaporation pond. Means and
standard deviations for three replicates are shown.
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The amount of Se volatilized by the cultures increased with the growth
of the cultures over time (Fig. 2 and 3).
Two of the Halomonas-like strains, MPD-51 and MPD-61, and
the M. saperdae-like strain (MPD-60), which grew well in the
selenate-supplied liquid medium, produced volatile Se at the highest
rates, 1.65, 1.09, and 0.88 µg of Se g of
protein
1 h
1,
respectively. The slow-growing bacterial isolates, i.e., those related
to "A. sanguineum " and B. firmus, exhibited
~5-fold lower rates of Se volatilization, 0.29 and 0.35 µg of Se g
of protein
1 h
1,
respectively, than the best Se volatilizer
Halomonas strain HTB0639-like MPD-51. Strain MPD-72, which is related to
Halomonas, grew well in the selenate-supplied medium, but
its rate of Se volatilization (0.16 µg of Se g of
protein
1 h
1) was only
10 to 15% that measured for its relatives, strains MPD-51 and MPD-61,
even though it accumulated a large amount of Se in the exponential
phase. However, the Se content of strain MPD-72 decreased once the
culture entered the stationary phase. The amount of Se accumulated by
strains MPD-51, MPD-60, and MPD-61 increased with the growth of the
cells over time (Fig. 2 and 3). These bacteria accumulated the most Se
by the end of the growth curve, whereas strains MPD-70 and MPD-67 did
not accumulate much Se over time. The total amounts of Se removed
(bioaccumulation plus volatilization) by strains MPD-51, MPD-60,
MPD-61, MPD-67, MPD-70, and MPD-72 at the end of the growth curve were
13.5, 17.68, 24.09, 3.72, 5.58, and 3.72 µg, respectively. Thus, two
strains closely related to Halomonas (MPD-51 and MPD-61) and
the strain related to M. saperdae (MPD-60) removed the
largest amount of Se from solution because they volatilized Se at the
highest rates and accumulated the most Se compared to the other
cultured bacterial strains.

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FIG. 3.
Amounts of Se volatilized or accumulated by cultures of
bacteria that were isolated from the selenium-contaminated solar
evaporation pond. Means and standard deviations for three replicates
are shown.
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In order to use the cultured bacterial strains for the bioremediation
of Se-contaminated drainage water, e.g., by bioaugmentation into
evaporation ponds, the bacteria need to tolerate the high concentrations of Se and salt which are often present in the ponds due
to fluctuating water levels. The ability of the bacteria to withstand
extremely high Se and salt concentrations was tested under control
conditions. The Halomonas-like strains (MPD-51, MPD-61, and
MPD-72) could tolerate 20% NaCl (a salinity of 422 mS
cm
1) and 0.2 mM selenate (16 mg of Se
liter
1), concentrations which are higher than
those measured in the evaporation pond brine at Red Rock Ranch in March
1997, when the samples were collected (34). These results
suggest that the Halomonas-like bacterial strains will
tolerate and survive at the very high Se and salt concentrations found
in evaporation ponds. Two of the three strains that were related to
Halomonas, strains MPD-51 and MPD-72, even grew at the
highest concentration of NaCl tested (Fig.
4). The B. firmus-like strain
MPD-67 and the M. saperdae-like strain MPD-60 grew at NaCl
concentrations of up to 10%, while the strain related to "A.
sanguineum," MPD-70, grew at NaCl concentrations of up to 5%.
With regard to selenate tolerance, most strains tolerated selenate
concentrations of up to 0.2 mM very well. There was still significant
growth for most strains at higher Se concentrations, and strain MPD-51
grew even at 2 M Se, a result which demonstrates its superior tolerance to Se.

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FIG. 4.
Effects of different concentrations of NaCl (left) and
selenate (right) on the growth of bacterial isolates from the
selenium-contaminated solar evaporation pond. Means and standard
deviations for three replicates are shown. Note that the different
selenate concentrations are plotted on a log scale. Growth was
estimated by measuring the absorbance of the cultures at 600 nm. The
absorbance of the culture immediately after inoculation was 0.005.
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XAS was used to determine the form of Se accumulated in the washed
bacterial cells. The near-edge spectra of Se in the bacterial pellets of strains MPD-51 and MPD-60 were similar to those of selenate,
with a low-energy shoulder on the selenate edge corresponding to a
component of organic Se (Fig. 5). In
comparison, strains MPD-61 and MPD-72 showed proportionally lower
levels of selenate and higher levels of organic species (Fig. 5). The
spectra of MPD-70 and MPD-67 were considerably more noisy due to their
lower selenium contents but appeared similar to those of MPD-51 and MPD-60 in having higher proportions of selenate. A quantitative analysis of the different forms of bioaccumulated Se was carried out
using an edge-fitting method with a mixture of selenate, selenite, SeMet, and elemental selenium (Table 3).
The edge fit showed that the major components of bioaccumulated Se were
similar to those of organic Se and selenate, with only small
contributions from selenite or elemental Se. The small fraction of
bioaccumulated Se identified as elemental Se in the cultures was
supported by the fact that none of the cultures contained the orange
color indicative of elemental Se at the end of the growth curve. Thus, it is very likely that the bacterial strains did not produce
significant amounts of elemental Se from selenate.

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FIG. 5.
Se K-edge X-ray absorption near-edge spectra for
bioaccumulated Se in four of the bacterial strains that were isolated
from the selenium-contaminated solar evaporation pond (A) compared to
aqueous selenate, selenite, and L-SeMet and solid red
elemental Se standards (B).
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TABLE 3.
Percent contributions to the fit for Se K-edge X-ray
absorption near-edge spectra for bacterial strains isolated from a
selenate-treated hypersaline evaporation pond (Fig.
5)a
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 |
DISCUSSION |
Despite the extreme conditions of the solar evaporation pond at
Red Rock Ranch (i.e., the high concentrations of Se and other elements
as well as various osmotic and heat stresses), the phylogenetic analysis showed that the pond supported a large diversity of
Bacteria. The dominant group in the pond was a previously
unaffiliated group of bacteria in the order Cytophagales.
The microbial community composition found in the present study was
strikingly similar to that found for two out of three limnologically
distinct hypersaline lakes in Antarctica; two of the lakes had clones
that grouped within Proteobacteria and
Cytophagales, while the microbial community of the third
lake was made up almost exclusively of Archaea
(5). Our analysis showed that there were no
Archaea in the 72 clones screened, a result which is
surprising because Archaea have been commonly found in
hypersaline environments (3, 4, 14). Results similar to
those of the present study were also found for a solar saltern, where
Bacteria constituted up to 25% of the microbial community
(2). These results, along with those for hyperthermophilic
communities containing Bacteria (16, 27), further support the view that Bacteria can exist in and
dominate some extreme environments that were previously assumed to
contain only Archaea.
Phylogenetic studies of extreme environments have revealed a wealth of
previously undiscovered microbial lineages (2, 16, 27).
The fact that the dominant group in the pond is a previously unaffiliated group of bacteria (Cytophagales) is an exciting
result because these bacteria may well have superior abilities for Se assimilation and volatilization and could therefore represent a source
of novel genes for Se bioremediation. However, none of the bacteria
belonging to this unaffiliated group could be cultured. Bacterial
strains that could be cultured mostly belonged to the
-Proteobacteria. This result is similar to that found for
a study of bacterial strains from a saltern in Spain, where most of the strains grouped in the
-Proteobacteria and belonged to
marine or halotolerant members of the genera Halomonas,
Deleya, Pseudomonas, Alteromonas,
Acinetobacter, and Vibrio (21).
There are two possible pathways for selenate metabolism by microbes,
dissimilatory selenate reduction (32), which immobilizes Se as elemental Se, and assimilation of selenate, which leads to the
formation of volatile Se. Dissimilatory selenate reduction takes place
mostly under anaerobic conditions (32), although there are
a few bacterial strains that carry out selenate reduction to elemental
Se under microaerophilic conditions (19). Because the pond
at Red Rock Ranch is largely aerobic in nature, it is unlikely that
selenate is metabolized by dissimilatory selenate reduction.
Furthermore, the data from the XAS analysis support the idea that the
bacterial strains mainly carry out assimilatory Se reduction to SeMet,
which could be methylated to Se-methylselenomethionine, which then
could be cleaved to form dimethylselenide. The aerobically grown
selenate-treated bacterial strains accumulated a mixture of
predominantly selenate and a SeMet-like species (Fig. 5 and Table 3),
analogous to the amino acid intermediates of the S assimilation
pathway. Elemental Se, the product of dissimilatory reduction of
selenate or selenite, did not make a substantial contribution to the
fits of the Se K-edge spectra (Table 3), in contrast with the results
of previous studies of anaerobically grown Rhodobacter
sphaeroides treated with selenite (37). Since dissimilatory selenate reduction can be ruled out as a significant metabolic pathway for the bacterial strains in the present study, the
culturable bacteria very likely use enzymes of the S assimilation pathway to assimilate and volatilize Se, in a manner similar to that of
plants (35).
The EC in the Red Rock Ranch evaporation pond fluctuates from 15 mS
cm
1 in the winter, when the pond is flooded by
rain, to 400 mS cm
1 in the summer
(34). Total Se levels in the pond can fluctuate from 3 to
45 mg liter
1. All the bacterial strains in the
present study tolerated NaCl concentrations of 5 to 10% (ECs of 79 to
148 mS cm
1) very well (Fig. 4). The salt
tolerance of all these strains was considerably higher than that of a
previously isolated Aeromonas strain, whose growth was
severely affected by an EC of 40 mS cm
1
(26). In fact, three of the cultured bacterial strains,
MPD-51, MPD-61, and MPD-72, all of which were related to
Halomonas species, were halotolerant, tolerating NaCl
concentrations of greater than 20% (Fig. 4).
The bacterial strains in the present study also tolerated Se
concentrations of up to 0.2 mM (~16 mg
liter
1), with significant growth at up to 20 mM
(~1,600 mg liter
1) (Fig. 4), a concentration
higher than the Se concentration in the salt from the pond (200 mg
liter
1) (Table 1). Strains MPD-51, MPD-60, and
MPD-67 grew at 200 mM selenate, and strain MPD-51 even grew at 2 M
selenate (~160 g liter
1) (Fig. 4). Thus, the
culturable bacteria isolated in the present study tolerated very high
concentrations of Se and NaCl, characteristics which make them good
candidates for Se bioremediation by bioaugmentation of evaporation
ponds or by treatment of hypersaline pond water in bioreactors.
The best strain for the bioremediation of hypersaline
selenate-contaminated solar evaporation ponds is most likely MPD-51, a
member of the Halomonas group that was the second most
dominant group in the pond. This is because it was the only cultured
bacterial strain that was halotolerant and tolerant of Se at
concentrations up to 2 M; it also accumulated, assimilated, and
volatilized Se at very high rates compared to the other cultured
bacterial strains. The rates of Se volatilization by
Halomonas-like strain MPD-51 (1.65 µg of Se g of
protein
1 h
1) supplied
with 70 µM selenate were ~300 to 3,000-fold higher than those
measured for Brassica juncea supplied with 100 µM selenate (8) and various wetland plants supplied with 20 µM
selenate (24). These rates were 100-fold higher than those
measured for an Aeromonas strain isolated from evaporation
pond water and cultured with 0.125 to 6.25 µM selenate to an optical
density similar to that of strain MPD-51 (26). Since
Halomonas-like strain MPD-51 grew under conditions of
various salinities and Se concentrations, the fluctuations in the salt
and Se levels caused by various water levels in solar evaporation ponds
should not affect its ability to survive or carry out Se
bioremediation processes under these conditions.
Solar evaporation ponds contain very high concentrations of S (Table
1), which is present mainly as sodium sulfate in agricultural drainage
water and in solar evaporation pond salt (6). Since the
physiological experiments (Fig. 3, 4, and 5) showed that the bacterial
isolates took up, assimilated, and volatilized Se (supplied as 70 µM
selenate or 5 mg of Se liter
1) at very high
rates in the presence of high concentrations of sulfate in the medium
(1 mM or 32 mg of sulfate liter
1), it is clear
that the culturable bacteria have a transporter(s) that can compete
effectively for selenate in the presence of sulfate. The gene for such
a transporter could prove useful in the genetic engineering of plants
for enhanced selenate uptake in the presence of sulfate. The
bioaccumulation of Se is of little practical significance for Se
bioremediation in that the microbial biomass is small and could not be harvested.
As stated earlier, volatilization is of particular interest for Se
bioremediation because it allows Se to be removed from the local food
chain into the atmosphere, where it is dispersed to other areas
(18); in California, this is not a problem because many
areas (e.g., the east side of the San Joaquin Valley) are known to be
deficient in Se and farm animals require Se supplementation. Volatilization may be enhanced by bioaugmentation with the rapidly volatilizing microbes (e.g., Halomonas-like strains MPD-51
and MPD-61) identified in the present study and by environmental
manipulation. The primary environmental factors that promote bacterial
Se volatilization are the addition of nutrients (especially C and N),
highly aerobic conditions, high temperatures (~35°C), high pHs
(~8), adequate moisture, Se forms and concentrations, and microbial
community composition (11). The water in the evaporation
pond at Red Rock Ranch is aerobic and has a pH of 8.5, a temperature of
>30°C for 8 months of the year, and high levels of nitrate (6,
34).
One factor that could be easily manipulated to increase Se
volatilization rates above those measured in the field is the addition of a carbon source. The availability of a carbon source is very likely
to affect Se volatilization because the production of volatile Se in the present physiological study paralleled the growth curve of
the bacterial isolates (Fig. 2 and 3). The addition of organic carbon
sources has been shown to significantly enhance the rates of microbial
Se volatilization in situ, sometimes up to 10-fold (11,
36). If the addition of an economical carbon source to the Red
Rock Ranch evaporation pond sustains the rates of Se volatilization that were measured in the physiological experiments, it may be possible
to remove most of the Se from the pond in an environmentally friendly,
relatively nontoxic manner.
 |
ACKNOWLEDGMENTS |
This work was supported by grants W08021-30 and W04163 from the
Electric Power Research Institute. The XAS analysis was performed at
SSRL, which is funded by the Department of Energy, Offices of Basic
Energy Sciences and Biological and Environmental Research, by the
National Institutes of Health, National Center for Research Resources,
Biomedical Technology Program, and by the National Institute of General
Medical Sciences.
We thank Zhiqing Lin for collecting samples of solar evaporation pond
salt and Marina Ma for technical assistance.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Plant and Microbial Biology, 111 Koshland Hall, University of
California, Berkeley, CA 94720-3102. Phone: (510) 642-3510. Fax: (510)
642-4995. E-mail: nterry{at}nature.berkeley.edu.
Present address: Department of Molecular, Cellular and
Developmental Biology, Campus Box 0347, University of Colorado,
Boulder, CO 80309-0347.
 |
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Applied and Environmental Microbiology, September 2001, p. 3785-3794, Vol. 67, No. 9
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.9.3785-3794.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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