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Applied and Environmental Microbiology, March 1999, p. 1133-1140, Vol. 65, No. 3
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Isolation from Estuarine Sediments of a
Desulfovibrio Strain Which Can Grow on Lactate Coupled to
the Reductive Dehalogenation of 2,4,6-Tribromophenol
Alfred W.
Boyle,
Craig D.
Phelps, and
L. Y.
Young*
Biotechnology Center for Agriculture and the
Environment, Rutgers, The State University of New Jersey, New
Brunswick, New Jersey
Received 17 September 1998/Accepted 28 December 1998
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ABSTRACT |
Strain TBP-1, an anaerobic bacterium capable of reductively
dehalogenating 2,4,6-tribromophenol to phenol, was isolated from estuarine sediments of the Arthur Kill in the New York/New Jersey harbor. It is a gram-negative, motile, vibrio-shaped, obligate anaerobe
which grows on lactate, pyruvate, hydrogen, and fumarate when provided
sulfate as an electron acceptor. The organism accumulates acetate when
grown on lactate and sulfate, contains desulfoviridin, and will not
grow in the absence of NaCl. It will not utilize acetate, succinate,
propionate, or butyrate for growth via sulfate reduction. When supplied
with lactate as an electron donor, strain TBP-1 will utilize sulfate,
sulfite, sulfur, and thiosulfate for growth but not nitrate, fumarate,
or acrylate. This organism debrominates 2-, 4-, 2,4-, 2,6-, and
2,4,6-bromophenol but not 3- or 2,3-bromophenol or monobrominated
benzoates. It will not dehalogenate monochlorinated, fluorinated, or
iodinated phenols or chlorinated benzoates. Together with its
physiological characteristics, its 16S rRNA gene sequence places it in
the genus Desulfovibrio. The average growth yield of strain
TBP-1 grown on a defined medium supplemented with lactate and
2,4,6-bromophenol is 3.71 mg of protein/mmol of phenol produced, and
the yield was 1.42 mg of protein/mmol of phenol produced when 4-bromophenol was the electron acceptor. Average growth yields (milligrams of protein per millimole of electrons utilized) for Desulfovibrio sp. strain TBP-1 grown with
2,4,6-bromophenol, 4-bromophenol, or sulfate are 0.62, 0.71, and 1.07, respectively. Growth did not occur when either lactate or
2,4,6-bromophenol was omitted from the growth medium. These results
indicate that Desulfovibrio sp. strain TBP-1 is capable of
growth via halorespiration.
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INTRODUCTION |
The field of microbially mediated
reductive dehalogenation has made tremendous strides in recent years,
largely due to the isolation of a number of anaerobic bacteria that
possess the ability to couple the reductive dehalogenation of aromatic
and aliphatic compounds to growth. The isolation of the first
halorespiring bacterium, Desulfomonile tiedjei, resulted in
a new genus (7), and since then a number of other
halorespiring bacteria have been isolated (2, 5, 14, 17, 21, 24,
27, 27a, 36, 37, 43). A number of these new isolates have brought
about the definition of new genera, including
Dehalococcoides (27), Dehalospirillum
(37), Desulfitobacterium (2, 4, 14, 27a, 36,
43), and Dehalobacter (17), while some
others have added to pre-existing genera, such as Pelobacter
(21).
The genus Desulfitobacterium contains six species of
halorespiring bacteria: Desulfitobacterium dehalogenans
(43), Desulfitobacterium frappieri
(2), Desulfitobacterium chlororespirans
(36), Desulfitobacterium hafniense
(4), Desulfitobacterium sp. strain PCE-S
(27a), and Desulfitobacterium sp. strain PCE1
(14). This genus is a member of the Clostridium
subphylum; hence, all members are gram positive and three of five
(Desulfitobacterium frappieri, Desulfitobacterium dehalogenans, and Desulfitobacterium chlororespirans)
are reported to form spores. All except strain PCE-S exhibit the
ability to dehalogenate ortho-substituted chlorines from phenols.
The other isolated halorespiring anaerobes fall into different genera,
most representing the delta and epsilon subdivisions of the
Proteobacteria (5, 7, 21, 37). Two interesting strains are Dehalobacter restrictus and
Dehalococcoides ethenogenes. Based upon 16S rRNA gene
sequence analysis, Dehalobacter restrictus falls into the
fourth subdivision of the gram positive bacteria, yet physiological and
biochemical analyses do not support its placement in this subdivision
(17). This organism will use only hydrogen or formate as an
electron donor and perchloroethene (PCE) or trichloroethene as an
electron acceptor and requires fermented yeast extract for growth.
Dehalococcoides ethenogenes is similarly metabolically
limited. It will utilize only hydrogen as an electron donor and PCE as
an electron acceptor and requires extracts from mixed microbial
cultures. Analysis of this organism's 16S rRNA gene sequence indicates
that it is a eubacterium, yet is not closely related to any known group
(27).
While halorespiring bacteria are phylogenetically diverse based upon
their 16S rRNA gene sequences, there is a lack of diversity with
respect to the types of compounds which can be dehalogenated. Typically
these organisms are capable of using only one of two classes of
halogenated compounds as electron acceptors for halorespiration: substituted, single-ring aromatic compounds (e.g., phenols and benzoates) or halogenated alkenes (e.g., PCE). Six of the twelve halorespiring organisms isolated, Desulfitobacterium sp.
strain PCE1, Desulfitobacterium frappieri,
Desulfitobacterium dehalogenans, Desulfitobacterium
chlororespirans, Desulfitobacterium hafniense, Desulfomonile tiedjei, and strain 2CP-1, are capable of
dehalogenating substituted aromatic compounds. Desulfomonile
tiedjei is also capable of dehalogenating PCE (11). In
addition, Desulfitobacterium sp. strain PCE1 can
dehalogenate PCE as well as ortho-chlorinated phenols
(14).
Although the substrates for these isolates can be divided into two
groups based upon their structure (aromatic or aliphatic), much
diversity exists with respect to the specific halogen group and the
position of halogenation of the target compound. For example, Desulfomonile tiedjei can utilize a variety of halogenated
compounds. It can dehalogenate brominated and iodinated benzoates and
benzamides regardless of the position of substitution; however, it will
remove only meta-substituted chlorines. Also, cell
suspensions of Desulfomonile tiedjei grown on
3-chlorobenzoate remove only meta-substituted chlorines from
polychlorinated phenols (28). Desulfitobacterium chlororespirans seems more selective than Desulfomonile
tiedjei. It will debrominate 2,4,6-tribromophenol (2,4,6-TBP) to
4-bromophenol (4-BP) but will not debrominate 2-BP. Likewise, it will
dechlorinate 2,4,6-trichlorophenol to 4-chlorophenol but will not
dechlorinate any monochlorinated phenol, nor will it dehalogenate
2-fluoro- or iodophenol. Desulfitobacterium chlororespirans
will also dechlorinate 2,3- (to 3-) and 2,6- (to 2-) dichlorophenol as
well as 3-chloro-4-hydroxy-benzoate and
3-chloro-4-hydroxy-phenylacetate (36). Strain 2CP-1
appears to have the most limited substrate range of the three. It will dehalogenate 2,6-di- and 2-chlorophenol but is incapable of
dehalogenating monosubstituted bromo-, fluoro-, or iodophenols in any
position (5). The differences in substrate specificity
between these organisms implies that differences exist with respect to
their dehalogenating enzymes.
All of the previously reported halorespiring anaerobic bacteria have
been isolated from soils, compost, sewage sludge, or sediments from
freshwater environments. Marine and estuarine sediments would seem to
be good sources of halorespiring bacteria given their exposure to
numerous brominated, iodinated, and chlorinated organic compounds
(12, 18, 35). In fact, reductive dehalogenation of
bromophenols (19, 30), bromobenzoates (30),
chlorophenols (26), and polychlorinated biphenyls
(1) has been demonstrated in marine and estuarine sediments.
A bacterium, strain DSL-1, that debrominates 2,4,6-TBP to 4-BP has been
isolated from sediments inhabited with bromophenol-producing marine
worms (39). In contrast to the halorespirers, this organism
does not couple the dehalogenation of 2,4,6-TBP to growth.
In this report we describe the enrichment and isolation of strain
TBP-1, a bacterium capable of reductive dehalogenation, from estuarine
sediments. This obligately anaerobic bacterium removes bromines
substituted in the ortho- and para-positions of
brominated phenols. It does not dehalogenate monochlorinated, fluorinated, or iodinated phenols. Physiological and molecular analyses
indicate that strain TBP-1 is a member of the genus
Desulfovibrio. Strain TBP-1 possesses the ability to grow by
coupling the oxidation of lactate to the reductive dehalogenation of
2,4,6-TBP.
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MATERIALS AND METHODS |
Enrichment preparation.
Anaerobic sediments from the Arthur
Kill in the New York/New Jersey harbor estuary (16) were
used as an inoculum. One hundred grams of previously collected sediment
(45) was diluted, under a mixture of nitrogen and carbon
dioxide (70:30), in 1.0 liter of anaerobic media composed of (in grams
per liter) KCl (1.3), KH2PO4 (0.2), NaCl
(21.0), NaHCO3 (7.5), NH4Cl (0.3),
CaCl2 · 2H2O (0.15),
MgCl2 · 6H2O (3.0), resazurin (0.001),
and Na2S · 9H2O (0.5); a 0.1-ml/liter
concentration of vitamin stock, containing (in milligrams per liter)
folic acid (20), pyridoxine HCl (100), riboflavin (50), biotin (20),
thiamine (50), nicotinic acid (50), pantothenic acid (50), vitamin
B12 (1.0), p-aminobenzoic acid (50), and thiotic
acid (50); and a 0.1-ml/liter concentration of metals stock (prepared
in dilute HCl), containing (in grams per liter)
H3BO4 (0.062), MnCl2 · 4H2O (0.098), FeCl2 · 4H2O
(1.49), CoCl2 · 6H2O (0.119),
NiCl2 · 6H2O (0.237), CuCl2
(0.134), and ZnCl2 (0.068). Thirty-milliliter aliquots of
this slurry were distributed in 60-ml serum bottles that had been
purged with N2-CO2. Bottles were crimp-sealed
with butyl rubber septa. Succinate was added from a sterile stock
solution to a final concentration of approximately 5 mM. Initial
2,4,6-TBP (Aldrich, Milwaukee, Wis.) addition and periodic
resupplementation to active enrichments were performed with a
concentrated stock solution prepared in 0.1 N NaOH. Each set of
conditions and controls were prepared in triplicate. All enrichments
and subsequent isolation and characterization experiments were
incubated statically in the dark at 30°C.
Isolation of strain TBP-1.
The medium used for all isolation
experiments was the same as that used for the initial enrichments.
Media prepared for isolation experiments were supplemented with acetate
(25 to 35 mM) and hydrogen. Hydrogen was supplied by evacuating
cultures under vacuum and repressurizing to 14 lb/in2 with
H2-CO2 (80:20). Soft agar shake tubes (28 ml,
total volume; 10 ml of medium) were prepared with Noble agar (Difco,
Detroit, Mich.) at a final concentration of 0.8%. Culture purity was
checked by phase-contrast light microscopy and confirmed by growth on medium D plus 2.5% NaCl (33), modified Baar's medium with
2.5% NaCl (15), and anaerobically prepared tryptic soy
broth (Difco).
Strain characterization.
Electron donors and acceptors used
for isolate characterization were added from concentrated aqueous
stocks to a final concentration of 10 mM unless otherwise indicated.
Elemental sulfur was added (0.1 ml per 10 ml) as an aqueous slurry. The
inocula for donor and acceptor experiments were grown with limiting
concentrations of lactate or sulfate, respectively, or centrifuged and
resuspended in anaerobic medium unamended with any donor or acceptor.
Strain TBP-1 was determined to be capable of utilizing various electron donors and acceptors based upon their ability to support growth (increase in total protein) and sulfate consumption (for donors) or
lactate consumption (for acceptors) relative to controls lacking either
donor or acceptor, depending upon the experiment. Each donor and
acceptor was tested in at least three separate experiments.
The various haloaromatics tested (see Table 1) were added from stocks
prepared in 0.1 N NaOH to a final concentration of 100 to 200 µM.
Cultures were supplied hydrogen and acetate or lactate as electron
donors and incubated for 7 to 10 days. Dehalogenated products (phenol
or benzoate) were assayed by high-pressure liquid chromatography
(HPLC). Compounds that were dehalogenated were added to cultures a
second time to ensure that activity could be maintained. The presence
of desulfoviridin was tested for by the technique of Postgate
(32). Gram staining was done by the modified Hucker method
(8).
Halorespiration experiments.
Strain TBP-1 was inoculated
into media supplemented with lactate (30 to 40 mM) and either
2,4,6-TBP, 4-BP, or sulfate. In addition, it was tested with lactate
alone and with 2,4,6-TBP alone. Cultures with lactate and bromophenols
were resupplemented with the appropriate bromophenol once or twice
daily for approximately 4 days after the onset of dehalogenating
activity. After the consumption of approximately 4 mM bromophenol or
sulfate, 20 ml of all cultures were centrifuged at 10,000 × g for 25 min, decanted, and resuspended in 1.0 ml of
sterile, unamended medium for protein analysis.
Analytical methods.
Sediment slurry (from enrichments) or
liquid-only (all other experiments) samples (0.5 to 1.0 ml) were drawn
through the stoppers by using degassed 1.0-ml sterile syringes with
16-gauge needles and centrifuged for 2 min in a benchtop
microcentrifuge. The supernatant was filtered with a
0.45-µm-pore-size Millex syringe filter (Millipore) prior to
analysis. All haloaromatics were measured with an HPLC (Beckman,
Fullerton, Calif.) equipped with a 4.6-mm by 25-cm Ultrasphere C18 column (Beckman) with UV detection. The initial
mobile-phase composition was 40% mobile phase A (40:57:3,
methanol-water-acetic acid) and 60% mobile phase B (80:18:2,
methanol-water-acetic acid) at a flow rate of 1.0 ml/min. This was
changed to 35% A-65% B over 5 min with a linear gradient. The mobile
phase was held at this composition for 5 min and then changed to 20% A
and 80% B over 2 min with a linear gradient. This condition was
maintained for another 11.5 min, at which point the analysis was
stopped. At 7.8 min in the run, the UV detector was switched from 280 to 295 nm to increase the sensitivity for the detection of the di- and
tribrominated phenols. The retention times (in minutes) under these
conditions were as follows: phenol, 4.5; 2-BP, 7.2; 4-BP, 9.1;
2.4-dibromophenol (2,4-DBP), 15.6; 2,6-DBP, 11.9; and 2,4,6-TBP, 21.5. Twenty-microliter injections were performed with an autosampler (Gilson
Medical Electronics, Inc., Middleton, Wis.).
Lactate and acetate were analyzed for with an HPLC (Beckman) equipped
with a 7.8-mm by 30-cm Rezex organic acids column (Phenomenex,
Torrance, Calif.) with UV detection at 210 nm. The mobile phase
consisted of 0.005 N H
2SO
4 at a flow rate of
0.5 ml/min. The column
was maintained at room temperature.
Twenty-microliter injections
were performed with an autosampler
(Gilson).
Sulfate analyses were performed on a Dionex (Sunnyvale, Ca.) model 100 ion chromatograph with an IonPac AS9 column by using
conductivity
detection. The eluant was 2 mM Na
2CO
3-0.75 mM
NaHCO
3 at 2.0 ml/min. The regenerant consisted of 25 mM
H
2SO
4 under He
at 8 lb/in
2.
Protein concentrations in unfiltered samples were determined by the
Bradford method (
3). Briefly, samples were diluted
1:1 in 2 N NaOH and incubated at 70°C for 45 min. Samples were
then
centrifuged in a benchtop microcentrifuge (3 min) and 100
µl was
reacted with 1.0 ml of dilute protein dye reagent (Bio-Rad,
Hercules,
Calif.). Absorbance at 595 nm was read after 5
min.
16S rRNA sequencing and analysis.
DNA was extracted from
cells (31) and further purified with a Gene-Clean kit (Bio
101) before amplification. 16S rDNA was amplified with the universal
eubacterial primers (27 Forward [5' AGA GTT TGA TCC TGG CTC AG 3']
and 1525 Reverse [5' AAG GAG GTG WTC CAR CC 3']) (22). The
following amplification parameters were used: initial denaturation at
95°C for 5 min, 20 to 30 cycles of 94°C for 0.5 min, 55°C for 0.5 min, and 72°C for 1.5 min, and a final extension at 72°C for 10 min, all amplified in a Gene Amp PCR system 2400 thermal cycler
(Perkin-Elmer, Foster City, Calif.).
The PCR product was purified with a QIAquick PCR purification kit
(Qiagen Inc., Chatsworth, Calif.), and the sequence was
determined by
automated techniques (Perkin-Elmer-ABI, Foster City,
CA) with the
following primers: 27 Forward (5' AGA GTT TGA TCC
TGG CTC AG 3'), 519 Reverse (5' GWA TTA CCG CGG CKG CTG 3'), 530
Forward (5' GTG CCA GCM
GCC GC GG 3'), 907 Reverse (5' CCG TCA
ATT CMT TTR AGT TT 3'), 926 Forward (5' AAA CTY AAA KGA ATT GAC
GG 3'), and 1492 Reverse (5' GGT
TAC CTT GTT ACG ACT T 3') (
22).
The complete sequence was aligned to related organisms with the
Ribosomal Database Project (
25) alignment function and
Genetic
Data Environment software, version 2.2 (
38).
Phylogenetic analysis
was performed by the neighbor-joining method with
programs in
the PHYLIP package, version 3.5c (
13). Bootstrap
values were
calculated with SEQBOOT, and a distance matrix was
constructed
with DNADIST employing a Kimura 2-parameter model and a
transition/transversion
ratio of 2.0. The tree was drawn with NEIGHBOR
and CONSENSE (
13).
Nucleotide sequence accession number.
The GenBank accession
number for the 16S rRNA gene sequence of strain TBP-1 is AF090830.
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RESULTS |
Enrichment and isolation of strain TBP-1.
Initial enrichment
cultures were inoculated with sediments from the Arthur Kill and
supplemented with succinate and 2,4,6-TBP. As seen in Fig.
1, complete debromination of 2,4,6-TBP to
phenol occurred prior to our first sampling point, which was at 19 days. No brominated intermediates were initially observed. Autoclaved controls exhibited no loss of 2,4,6-TBP and no production of phenol (data not shown). Dehalogenation to phenol continued after subsequent refeeding of 2,4,6-TBP. After the second resupplementation of 2,4,6-TBP, the rate of 2,4,6-TBP loss (debromination) slowed and partially debrominated intermediates (2,4-DBP and 4-BP) were observed to accumulate. The addition of succinate at 52 days resulted in the
rapid dehalogenation of these intermediates and the residual 2,4,6-TBP.
The transient accumulation of 2,4-DBP and 4-BP suggests that removal of
ortho-substituted bromines precedes
para-debromination. The rapid dehalogenation of
intermediates after succinate resupplementation suggests that the
debrominating system was carbon and/or electron limited.

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FIG. 1.
Dehalogenation of 2,4,6-TBP in enrichments inoculated
with Arthur Kill sediments and supplemented with succinate. Closed
circles, 2,4,6-TBP; open circles, phenol; squares, 4-BP; triangles,
2,4-DBP. Dotted lines are used to indicate that these lines do not
represent actual rates of activity since all of the 2,4,6-TBP was
consumed prior to our first sampling point after feeding. Data are the
average of triplicates, and error bars represent 1 standard deviation.
Arrow indicates time of succinate resupplementation. Sterile controls
did not exhibit 2,4,6-TBP loss or phenol production (data not shown).
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At 114 days one of the replicate enrichment cultures was serially
diluted to 10
12 in anaerobic media supplemented with
2,4,6-TBP and hydrogen and
acetate. Succinate was replaced as the
carbon and electron donor
in all further isolation activities in an
attempt to minimize
the growth of nonhalorespiring bacteria. The
highest dilution
to express dehalogenating activity after 51 days of
incubation
(10
5) was further diluted 1,000-fold. This
culture was incubated for
9 days and then diluted yet again by a factor
of 10. After growing
for 29 days with periodic refeeding of 2,4,6-TBP
this culture
was serially diluted into anaerobic shake tubes containing
0.8%
Noble agar. The shake tubes were incubated for 18 days, after
which point nine colonies were picked, two from the 10
3
dilution and seven from the 10
2 dilution. All had the
same off-white, diffuse, round morphology.
Eight of the nine colonies
expressed dehalogenating activity.
One isolate was chosen for further
study and designated TBP-1.
Purity was checked by culturing the isolate
on a variety of complex
anaerobic media (see Materials and Methods).
Under all growth
conditions only one cellular morphology was observed,
as determined
by phase-contrast light
microscopy.
Initial characterization of strain TBP-1.
Strain TBP-1 is a
gram-negative, vibrio-shaped bacterium approximately 1 by 4 µm in
size (Fig. 2). It is motile and tested positive for the presence of desulfoviridin, suggesting that it is a
member of the genus Desulfovibrio. Older cultures of TBP-1 do not appear to form spores; however, they undergo distinct
morphological changes. As the culture ages, the cells change from a
vibrio shape to a spherical form which appears to be devoid of a cell
wall. These observations are consistent with morphological variations observed with a number of Desulfovibrio species
(33). Growth did not occur on modified Baar's medium with
2.5% NaCl when the culture was incubated statically with a headspace
of air rather than argon, indicating that strain TBP-1 cannot grow
aerobically.

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FIG. 2.
Phase-contrast light micrographs of strain TBP-1 grown
on lactate and sulfate. Spherical body illustrates morphological
transformation that occurs in older cultures. Bar, 5 µm.
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The effects of various NaCl concentrations on the growth of strain
TBP-1 on modified Baar's medium at 30°C are illustrated
in Fig.
3. The highest growth rate (0.20 h
1) and yield were achieved with 3.75% NaCl. The
specific growth
rates with 1.25, 2.5, 5.0, and 7.5% NaCl were 0.16, 0.17, 0.09,
and 0.07 h
1, respectively. Growth occurred
after 10 h of incubation in cultures
with 1.25, 2.5, and 3.75%
NaCl, while lag periods of 19 and 50
h were observed prior to the
onset of growth for the 5.0 and 7.5%
NaCl cultures, respectively. No
growth occurred in the absence
of NaCl.

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FIG. 3.
Growth of strain TBP-1 on modified Baar's medium at
30°C with increasing concentrations of NaCl (indicated for each
curve). Data are the averages of duplicates.
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Various electron donors and acceptors were tested for their ability to
support the growth of strain TBP-1. Lactate, pyruvate,
fumarate,
formate, and hydrogen supported sulfate consumption
and growth. All of
these donors except fumarate (not tested) support
dehalogenation of
2,4,6-TBP. Acetate accumulates in the culture
medium when strain TBP-1
is provided lactate and sulfate, indicating
that it is an incomplete
oxidizer. Acetate, propionate, butyrate,
and succinate do not support
growth, sulfate reduction, or debromination
of 2,4,6-TBP. Sulfate,
sulfite (5 mM), thiosulfate, and sulfur
support lactate consumption and
growth, while nitrate, acrylate,
and fumarate do
not.
The ability of strain TBP-1 to dehalogenate a variety of substituted
phenols and benzoates was examined and summarized in
Table
1. Only brominated phenols with bromines
in the
ortho and/or
para position were
dehalogenated. The bromine in the
ortho position
of
2,3-bromophenol was not removed. Furthermore, none of the other
halogenated aromatics could serve as substrates. These results
suggest
that only bromines in the
ortho or
para positions
will
be removed and that
meta-substituted bromines prevent
the dehalogenation
of adjacent
ortho-substituted bromines.
Growth via halorespiration.
Figure
4 shows that strain TBP-1 consumes
2,4,6-TBP with the stoichiometric accumulation of phenol. Duplicate
cultures were refed 2,4,6-TBP a total of 10 times, each refeeding
occurring after the complete consumption of the previous addition. The
cumulative amount of 2,4,6-TBP consumed is plotted against the
cumulative amount of phenol produced. The slope of the regression line
is 0.94, indicating stoichiometric conversion of 2,4,6-TBP to phenol. Stoichiometric production of phenol also demonstrates that no abiotic
loss of phenol occurred. Similarly, phenol loss has never been observed
in cultures of TBP-1. The medium contained only bicarbonate and
bromophenol as potential electron acceptors. Since no methane was
produced we postulated that dehalogenation was occurring by one of two
mechanisms: either tribromophenol was serving as an electron acceptor
in halorespiration and was required for growth on lactate, or the
organism was growing fermentatively on lactate and dehalogenating the
bromophenol by a mechanism that was not linked to growth.

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FIG. 4.
Stoichiometric dehalogenation of 2,4,6-TBP to phenol by
strain TBP-1. Dotted line represents the regression line of the average
cumulative 2,4,6-TBP consumed by duplicate cultures plotted against the
average cumulative phenol produced. Stoichiometric phenol production
demonstrates that dehalogenation of 2,4,6-TBP was complete and that no
phenol was consumed by or lost from these cultures.
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In order to test these hypotheses, strain TBP-1 was grown in the
presence of excess lactate (approximately 38 mM) and one
of the
following: sulfate, 2,4,6-TBP, or 4-BP. The bromophenols
were added
once or twice daily (0.4 to 0.5 mM) to avoid high levels
(>1.5 mM),
which we have observed to be toxic to TBP-1. The initial
sulfate
concentration was 4.5 mM. The results from this experiment
are shown in
Table
2. Cultures incubated with only
lactate or
2,4,6-TBP failed to grow, indicating that TBP-1 can neither
grow
fermentatively on lactate or 2,4,6-TBP nor dehalogenate 2,4,6-TBP
in the absence of an electron donor.
When TBP-1 was grown on 2,4,6-TBP, the average growth yield, 3.71 mg of
protein per mmol of phenol produced, was 2.6 times
that obtained when
it was grown on 4-BP (1.42). Since this is
reasonably close to the
increase in number of bromines removed
per molecule, it indicates a
proportional increase in the electrons
transferred and hence the energy
available. This is further underscored
by the similarity in average
growth yields, 0.71 and 0.62, when
the growth yields are normalized to
millimoles of electrons transferred
for growth on 4-BP and 2,4,6-TBP,
respectively. Therefore, growth
of strain TBP-1 in the presence of
brominated phenols and lactate
is dependent upon dehalogenation, and
growth increases proportionally
with the number of bromines removed. In
contrast, the average
growth yield per millimole of electrons with
sulfate (1.07) is
higher than with brominated phenols (0.67, average of
2,4,6- and
4-BP
results).
Phylogeny.
The morphological and physiological characteristics
of strain TBP-1 suggest that it is a member of the genus
Desulfovibrio. This is further supported by the organisms
16S rRNA gene sequence. Sequence analysis of 1,435 bp indicates that
strain TBP-1 is a member of the delta subdivision of the
Proteobacteria within the family
Desulfovibrionaceae (Fig. 5)
(6). Strain TBP-1 clustered with members of the genus
Desulfovibrio, with its closest relative being
Desulfovibrio acrylicus (98.9%).

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FIG. 5.
Phylogenetic tree of strain TBP-1 and other related
species based on 16S rRNA gene sequences. Bootstrap values at nodes are
the percentages of 100 iterations. Values less than 50% are not
included. The scale bar indicates the estimated number of substitutions
per 100 positions.
|
|
 |
DISCUSSION |
Strain TBP-1, isolated from sediments of the New York/New Jersey
harbor estuary, is an obligately anaerobic bacterium capable of
reductively dehalogenating ortho- and
para-substituted bromophenols. Growth of strain TBP-1 on
lactate depends on the presence of NaCl and a suitable electron
acceptor. When 2,4,6-TBP and 4-BP are used as electron acceptors,
growth occurs and stoichiometric levels of phenol are produced. Growth
does not occur in the absence of a utilizable electron acceptor and
neither dehalogenation nor growth occurs when strain TBP-1 is incubated
with only 2,4,6-TBP. These results therefore demonstrate that strain
TBP-1 can grow via halorespiration.
In comparison to other halorespiring organisms, TBP-1 has a low growth
yield when it uses bromophenols (0.67 mg of protein per mmol of
electrons utilized for dehalogenation). For example, growth yields for
Desulfitobacterium sp. strain PCE1 (on
3-chloro-4-hydroxybenzoate), Desulfomonile tiedjei (on
3-chlorobenzoate), and Dehalobacter restrictus (on PCE) were
reported to be 0.8 (14), 1.05 (17), and 1.4 (29) mg of protein/mmol of electrons utilized, respectively. Likewise, yields ranging from 1.6 to 5.65 mg of cells (dry weight) per
mmol of electrons utilized (originally reported as grams per mole of
electron pairs utilized) were obtained for Desulfitobacterium dehalogenans (23). Mackiewicz and Weigel indicated
that, assuming that the protein yield is 50% of the total dry-weight
biomass, this range of values (0.8 to 2.83 g of protein per mol of
electrons utilized) agrees with those obtained for Desulfomonile
tiedjei and Dehalobacter restrictus.
There are a number of possible explanations for the observed
differences in growth yield. On a thermodynamic basis, the structure of
the halogenated compound dictates the amount of energy available from
the cleavage of a carbon-halide bond. For instance, the dechlorination of monosubstituted anilines (124.6 kJ/reaction when hydrogen is used as
the electron donor) and 2-hydroxy-5-chlorobenzoate (144.4 kJ/reaction)
yields approximately 22 and 10% less energy, respectively, than the
dechlorination of monosubstituted phenols (160.7 kJ/reaction) (10,
41). This suggests that growth yield differences between halorespirers may be the result of structural differences between, and
thus the amount of energy available from, the halogenated electron acceptors.
In addition, different experimental techniques may also contribute to
the observed differences in growth yield. Mohn and Tiedje (29) discussed the possibility that the differences in
growth rate and yield they observed and the values obtained by Dolfing (9) for Desulfomonile tiedjei were a result of
differences in medium composition. Indeed, the cell yield data we
report may be a result of suboptimal salinity. Further characterization
of TBP-1 on modified Baar's medium indicated that optimal growth took
place at 3.75% salinity, not 2%, which was used in the yield experiments.
Variations in the reported growth yields may also be a result of the
age at which the cultures were harvested for biomass determinations.
Mackiewicz and Wiegel reported a nonlinear relationship between
measured growth and amount of substrate utilized for
Desulfitobacterium dehalogenans. The authors speculated that
the decrease in growth yield with increasing culture age was a result
of higher maintenance energy demands during late exponential growth
than in early exponential growth (23). In comparison, the
values for Desulfomonile tiedjei, Dehalobacter
restrictus, and Desulfitobacterium sp. strain PCE1 were
made as endpoint measurements with all cultures apparently in some
stage of stationary growth.
Finally, it is possible that periodic limitation of substrate
(2,4,6-TBP) caused discontinuous, and thus less efficient, growth of
TBP-1, resulting in the relatively lower growth yield. Despite resupplementation of the cultures twice daily, 4-BP and 2,4,6-TBP were
at times limiting during the course of the experiment. The observation
that higher growth yields for TBP-1 were obtained on sulfate, an
energetically less favorable acceptor (10, 42) that was in
excess, than on 2,4,6-TBP and 4-BP, is consistent with this hypothesis.
In addition, yields for Desulfitobacterium dehalogenans with
fumarate, nitrate, sulfite, and 3-chloro-4-hydroxyphenylacetate as
electron acceptors, provided in excess, were similar (25.9, 23.8, 23.3, and 24.2 g of biomass/mol of ATP formed) (23),
suggesting that for strain TBP-1, 2,4,6-TBP limitation may indeed have
contributed to the lower growth yields. While numerous factors may be
involved in determining the cellular yields for these different
bacteria growing with halogenated substrates as terminal electron
acceptors, it is clear that all of these microorganisms are capable of halorespiration.
Morphological, physiological, and phylogenetic characteristics support
the placement of strain TBP-1 in the genus Desulfovibrio. It
also has high (98.9%) 16S rRNA gene sequence homology to
Desulfovibrio acrylicus. The latter organism was isolated
from marine sediments based upon its ability to cleave
dimethylsulfoniopropionate and couple the reduction of acrylate to
growth (44). Desulfovibrio sp. strain TBP-1 does
not reduce acrylate. Furthermore, Desulfovibrio sp. strain
TBP-1 grows on fumarate and sulfate while Desulfovibrio acrylicus does not. Also, while TBP-1 can grow on modified Baar's medium with 7.5% NaCl, Desulfovibrio acrylicus cannot grow
on lactate and acrylate with more than 4% NaCl in the growth medium. These two strains therefore, have several key differences. Whether they
should be considered separate species would depend on further physiological and molecular comparisons.
The types of halogenated electron acceptors used by
Desulfovibrio sp. strain TBP-1 is limited. It will use only
bromophenols with bromines in the ortho and/or
para position without adjacent bromines. It sequentially
dehalogenates 2,4,6-TBP to phenol. On the other hand,
Desulfitobacterium chlororespirans (36) and strain DSL-1 (39) both only partially dehalogenate 2,4,6-TBP to 4-BP. Furthermore, Desulfitobacterium chlororespirans, a
halorespiring bacterium, cannot dehalogenate 2-BP even though it
removes the ortho-substituted bromines from 2,4,6-BP
(36). In contrast, strain DSL-1 is reported to be a
fermentative bacterium which grows only on yeast extract and
constitutively expresses debrominating activity (39). The
different degrees of substrate specificity exhibited by the various
debrominating strains suggests broad diversity with respect to their
dehalogenating enzymes.
The identification of dehalogenating activity in marine environments
(1, 19, 30) suggests that marine and estuarine systems are
potentially sources of halorespiring bacteria. The isolation of
Desulfovibrio sp. strain TBP-1, a salinity-dependent halorespiring bacterium, from estuarine sediments supports this likelihood. It is interesting that based on recent phylogenetic evidence, other dehalogenating bacteria related to TBP-1 may be present
in marine and estuarine environments. For example, an isolate from San
Francisco Harbor dechlorinates 2,6-di- and 2-chlorophenol and has been
tentatively identified as a Desulfovibrio (based upon 16S
rRNA sequence); however, it utilizes acetate for growth (40). It also cannot dehalogenate bromophenols. In addition, four distinct clones from a highly enriched Arthur Kill sediment culture which dehalogenates 2-BP were obtained from a library generated
by amplification of the 16S rRNA genes. One of the four clones has high
sequence homology to members of the genus Desulfovibrio while a second has homology to members of the family
Desulfobacteriaceae (20). Similarly, molecular
characterization of a highly enriched 2,3,5,6-tetrachlorobiphenyl-dechlorinating community inoculated with
Baltimore Harbor sediments indicates the presence of members of the
delta subdivision of the Proteobacteria (34). The
organisms responsible for the dehalogenation reactions in the
enrichments of Knight et al. (20) and Pulliam Holoman et al.
(34), however, have not been determined. The reports of
various dehalogenating cultures from marine and estuarine sediments
suggest that these environments are an underexplored source of
anaerobic bacteria with diverse dehalogenating capabilities.
 |
ACKNOWLEDGMENTS |
We thank Norberto Palleroni for photographing strain TBP-1; Lee
Kerkhof and Victoria Knight for assisting in phylogenetic analyses;
Imelda Harjono, Vivian Chu, and Roza Wojcik for technical assistance;
and Beau Ranheim, the crew of Osprey (New York City Department of
Environmental Protection), and Monica Togna for sediment collection.
This research was funded, in part, by grants R-823575 and R-819679 from
the United States Environmental Protection Agency.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Biotech Center,
Foran Hall, Cook College, Rutgers, The State University of New Jersey, 59 Dudley Rd., New Brunswick, NJ 08901-8520. Phone: (732) 932-8165, ext. 312. Fax: (732) 932-0312. E-mail:
Lyoung{at}aesop.rutgers.edu.
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