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Applied and Environmental Microbiology, June 2001, p. 2622-2626, Vol. 67, No. 6
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.6.2622-2626.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Complete Denitration of Nitroglycerin by Bacteria
Isolated from a Washwater Soakaway
Samantha J.
Marshall* and
Graham F.
White
School of Biosciences, Cardiff University,
Cardiff CF10 3US, United Kingdom
Received 27 November 2000/Accepted 3 April 2001
 |
ABSTRACT |
Four axenic bacterial species capable of biodegrading nitroglycerin
(glycerol trinitrate [GTN]) were isolated from soil samples taken
from a washwater soakaway at a disused GTN manufacturing plant. The
isolates were identified by 16S rRNA gene sequence homology as
Pseudomonas putida, an Arthrobacter species, a
Klebsiella species, and a Rhodococcus species.
Each of the isolates utilized GTN as its sole nitrogen source and
removed nitro groups sequentially from GTN to produce glycerol
dinitrates and mononitrates (GMN), with the exception of the
Arthrobacter strain, which achieved removal of only the
first nitro group within the time course of the experiment. The
Klebsiella strain exhibited a distinct preference for
removal of the central nitro group from GTN, while the other five
strains exhibited no such regioselectivity. All strains which removed a
second nitro group from glycerol 1,2-dinitrate showed regiospecific
removal of the end nitro group, thereby producing glycerol
2-mononitrate. Most significant was the finding that the
Rhodococcus species was capable of removing the final nitro group from GMN and thus achieved complete biodegradation of GTN. Such
complete denitration of GTN has previously been shown only in mixed
bacterial populations and in cultures of Penicillium corylophilum
Dierckx supplemented with an additional carbon and nitrogen
source. Hence, to the best of our knowledge, this is the first report
of a microorganism that can achieve complete denitration of GTN.
 |
INTRODUCTION |
For most of the 20th century,
nitroglycerin (glycerol trinitrate [GTN]) has been a major explosive
for both military and civilian applications, and production facilities
have been established throughout the world. Synthesis of GTN involves
direct nitration of glycerol with nitric acid (with sulfuric acid as a
catalyst). The low solubility of GTN in water is exploited in the
washing of GTN oil with aqueous media to free the product from residual mineral acids and ions. The washing wastewaters, saturated with GTN
(ca. 8 mM) and bearing suspended droplets of GTN, have commonly been
transferred to lagoons or soakaways, resulting in actual or potential
contamination of soils. However, at the soakaways used for over 80 years at what was once the second largest commercial explosive
manufacturing plant in the world, recent extensive site investigation
and analysis of soils (10) have shown a remarkable absence
of detectable GTN (R. Morris, personal communication).
In recent years, the first discovery and isolation of GTN-degrading
bacteria in activated sewage sludge, river water, and soils
(18) led to similar work by other workers in Europe and the United States. Thus, bacteria able to utilize GTN as a sole source
of nitrogen are now well known (3, 4, 9, 16, 17, 19).
Although several of these bacterial strains were capable of removing
either one or two nitro groups from GTN to form glycerol dinitrates
(GDN) and glycerol mononitrates (GMN), none was able to biodegrade GMN
and thus achieve complete mineralization. However, complete
biodegradation has been observed in mixed bacterial cultures (1,
15) and fungi (20). Moreover, an analysis of
theoretical energy yields, based on entirely reasonable assumptions about the catabolic pathway of GTN, has shown that GTN should be
capable of supporting aerobic and anaerobic growths (12).
With these points in mind, we undertook a search for the presence in
soakaway soils of bacteria capable of effecting a complete degradation
of GTN. The study not only yielded the first known examples of a single
strain which could achieve complete denitration of GTN but also
expanded the list of known species capable of utilizing GTN as a sole
nitrogen source.
 |
MATERIALS AND METHODS |
Materials.
A stock solution of GTN (5% [vol/vol] in
ethanol) was kindly provided by EXCHEM, Derbyshire, United Kingdom.
Unless stated otherwise, all chemicals were obtained from Fisher
Scientific, Loughborough, Leicestershire, United Kingdom.
High-purity water (18 M
, filtered through 0.22-µm-pore-size
filters) from a Milli-Q50 system (Millipore, Watford, United Kingdom)
was used for the preparation of aqueous high-pressure liquid
chromatography (HPLC) eluents and for rinsing eluent-containing glassware. HPLC grade methanol of far UV grade quality was obtained from Fisher Scientific. Helium and compressed air, for operating the
HPLC system, were from BOC, London, United Kingdom.
Taq polymerase and deoxynucleoside triphosphates were
obtained from Promega, Southampton, United Kingdom, and New England
Biolabs Ltd., Hitchin, United Kingdom, respectively. PCR primers
were
synthesized by GIBCO BRL, Life Technologies Ltd., Paisley,
United
Kingdom.
Culture media.
Basal salts medium comprised the following
(per liter): K2HPO4, 3.5 g;
KH2PO4, 1.5 g; NaCl, 0.5 g;
MgSO4, 0.12 g; and 1 ml of trace elements solution.
The trace elements solution contained the following (grams per liter):
sodium borate, 0.57; FeCl3 · 6H2O, 0.24;
CoCl2 · 6H2O, 0.04;
CuSO4 · 5H2O, 0.06;
MnCl2 · 4H2O, 0.03;
ZnSO4 · 7H2O, 0.31; and
Na2MoO4 · 2H2O, 0.03. After
being autoclaved and cooled, the basal salts medium was amended with 1% (vol/vol) glycerol and GTN (from the ethanolic working stock solution).
Bacteria were also grown and maintained on nutrient broth and nutrient
agar, made up according to the manufacturer's instructions
(Difco
Laboratories, Detroit, Mich.).
Isolation, maintenance, and growth of bacteria.
Bacteria
capable of growth at the expense of GTN as the sole nitrogen source
were isolated from four soil samples (SP1a, SP1b, SP2, and SP3) taken
from a washwater soakaway at a disused GTN manufacturing plant in
Somerset West, South Africa. For each enrichment culture, a sample (25 g) of soil was added to 250 ml of basal salts medium containing 1%
(vol/vol) glycerol as a carbon source and 0.2 mM GTN as the sole
nitrogen source. After incubation at 30°C and shaking at 100 rpm for
2 weeks, a 5-ml portion was diluted into 250 ml of fresh growth medium.
A further three serial subcultures were made at approximately weekly
intervals, using a 1% (vol/vol) inoculum. Bacterial growth in liquid
cultures was monitored by measuring the optical density of the medium
at 540 nm. Samples from the final enrichment flask were serially
diluted and spread onto nutrient agar plates to allow visible colonies
to develop from single bacteria. Single colony types were separated and
subcultured onto fresh nutrient agar plates to purity.
Strains were maintained on nutrient agar slopes and plates with regular
transfers onto fresh medium. For long-term storage,
strains were stored
at

70°C in Protect Bacterial Preservers (Technical
Service
Consultants, Heywood, Lancashire, United
Kingdom).
Identification of bacteria.
Bacteria were identified using
16S rRNA gene sequence homology. Genomic DNA was obtained from bacteria
grown overnight at 30°C in 5 ml of nutrient broth. Cells were
harvested from 1 ml of culture by centrifugation and resuspended in 100 µl of sterile water. The cell suspension was heated at 94°C in a
Primus Thermocycler (MWG-Biotech, Ebersberg, Germany) to lyse the cells
and release the genomic DNA. Cell debris were removed by centrifugation
at maximum speed in a microcentrifuge for 5 min, and the supernatant was utilized as the template in the PCR.
The PCR mixture consisted of 0.2 to 1.0 µl of the genomic DNA
template solution, 1× PCR buffer, 1.5 mM MgCl
2, 100 ng
each
of primers 63f (5' CAG GCC TAA CAC ATG CAA GTC 3') and
1387r (5'
GGG CGG WGT GTA CAA GGC 3') (
8), 0.2 mM each of dATP, dCTP,
dGTP, and dTTP, and 0.25 U of
Taq
polymerase in a final volume
of 25 µl. Thermal cycling was undertaken
by initially denaturing
the DNA at 96°C for 5 min, followed by 30 cycles of 96°C for 30
s, 55°C for 30 s, and 72°C for
30 s and finally 72°C for 5 min.
A portion of the reaction
mixture was used to visualize PCR products
on 1% (wt/vol) agarose
gels. PCR products in the remainder of
the reaction mixture were
purified using a QIAquick PCR purification
kit (QIAGEN, Ltd., Crawley,
West Sussex, United Kingdom) and sequenced
using an ABI PRISM BigDye
terminator cycle ready reaction kit
according to the manufacturer's
instructions (PE Applied Biosystems,
Warrington, United Kingdom).
Sequence data obtained were compared
with known 16S rDNA sequences
using the BLAST algorithm at
http://www.ncbi.nlm.nih.gov/BLAST/ (
2).
Growth studies.
Each of the six axenic strains was grown at
30°C in basal salts medium containing 1% (vol/vol) glycerol and 0.2 mM GTN to create a starter culture which could be used as an inoculum.
Aliquots (1 ml) of each of these starter cultures were transferred to
100 ml of fresh medium, and growth was monitored by measuring the optical density at 540 nm. When necessary, samples (1 ml) were removed
at intervals during growth and centrifuged to remove bacterial cells
and the supernatant was stored at
70°C for subsequent analysis of
nitrate ester content. Concentrations of GTN and its potential biodegradation products, glycerol 1,3-dinitrate (1,3-GDN), glycerol 1,2-dinitrate (1,2-GDN), glycerol 1-mononitrate (1-GMN), and glycerol 2-mononitrate (2-GMN) were measured by HPLC.
HPLC analysis of nitrate esters.
Samples (1 ml) were
filtered through 0.2-µm-pore-size Anotop IC filters (Whatman,
Maidstone, United Kingdom). HPLC analysis of the filtrate was performed
using a DX300 series ion chromatograph unit (Dionex, Camberley, United
Kingdom) consisting of an advanced gradient pump (AGP-1) and basic
chromatography module with a 50-µl injection loop, linked to a
variable-wavelength UV detector via a Lichrosorb ODS column (250 by 4.6 mm, 10-µm bead) fitted with a 10-mm guard column (Phase Separations,
Deeside, United Kingdom). Nitrate esters were separated using a
programmed gradient of 5% (vol/vol) methanol in water for 5 min,
followed by a linear gradient of 5 to 50% (vol/vol) methanol over 30 min, and finally 50% (vol/vol) methanol for 5 min at a flow rate of 1 ml/min. Column effluents were monitored by UV at
A217. The system was calibrated using authentic
GTN, 1,3-GDN, 1,2-GDN, 1-GMN, and 2-GMN standards (Radian International, Austin, Tex.).
 |
RESULTS |
Isolation and identification of bacteria capable of GTN
biodegradation.
Standard enrichment techniques initially yielded
7, 8, 5, and 6 different colony types from soils SP1a, SP1b, SP2, and
SP3, respectively. Each of the 26 isolates obtained was reinoculated into basal salts medium containing both GTN and glycerol to test the
ability of the axenic strains for growth on GTN as the sole source of
nitrogen. Growth within 1 to 2 days was observed for six of the axenic
strains isolated, namely strains SP1a-2 (i.e., isolate number 2 from
sample SP1a), SP1b-5, SP1b-6, SP2-4, SP2-5, and SP3-4. These six axenic
strains capable of effecting GTN biodegradation were identified by 16S
rRNA gene sequence homology (Table 1). Other strains showed no growth over a period of 5 days.
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TABLE 1.
Identification by 16S rRNA gene sequence homology of
axenic strains which grow at the expense of GTN as a sole source of
nitrogen
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|
Biodegradation of GTN by axenic strains.
Starter cultures of
each of the six axenic strains were prepared by growth for 5 days at
30°C in basal salts medium containing 1% (vol/vol) glycerol and 0.2 mM GTN as the sole source of nitrogen. Aliquots (1 ml) of each starter
culture were transferred axenically into 100 ml of fresh, like medium,
and the growth and biodegradation of GTN and its metabolites were monitored.
Pseudomonas putida strains SP1a-2 and SP1b-6.
Although the growth of strain SP1a-2 was relatively slow over the 60-h
time course studied (Fig. 1), complete
disappearance of GTN occurred within the first 18 h of the
experiment. GTN was converted into a mixture of 1,3-GDN and 1,2-GDN in
a ratio of approximately 1 to 2 (the same ratio as the relative
concentrations of central and terminal groups), indicating random
removal of either the central or one of the two equivalent terminal
groups. Conversion of the dinitrates to mononitrates occurred more
slowly, with the 1,2-GDN being converted more rapidly to the
mononitrates than was the 1,3-GDN. As a result, the final
1,3-GDN/1,2-GDN/1-GMN/2-GMN ratio in the growth medium was
approximately 2 to 1 to 3 to 4 at the end of the experiment (Table
2). The yield of 2-GMN accounted for most
of the 1,2-GDN formed, indicating little conversion of the latter to
1-GMN. The total concentration of nitrate esters in the growth medium
did not diminish over the time course of the experiment (Fig. 1),
showing an inability of this strain to degrade either of the GMN
isomers.

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FIG. 1.
Biodegradation of GTN by P. putida strain
SP1a-2 showing bacterial growth (a) and concentration of nitrate esters
(b). Symbols: , GTN; , 1,3-GDN; , 1,2-GDN; , 1-GMN; ,
2-GMN; , total nitrate esters. O.D.540, optical density
at 540 nm.
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|
Although identified as the same species, strain SP1b-6 grew slightly
faster than SP1a-2 during the middle phase (18 to 36
h) of growth,
and this coincided with a more rapid conversion
of 1,2-GDN to the
mononitrates (data not shown). Apart from this
difference, the
biodegradation profiles of the two strains were
similar, i.e., complete
disappearance of GTN within the first
18 h of the experiment,
production of 1,3-GDN and 1,2-GDN occurring
in a ratio of 1 to 2, the
same regioselective removal of the end
nitro group from 1,2-GDN, much
slower conversion of 1,3-GDN to
the mononitrates than that of 1,2-GDN,
and the total molar concentration
of nitrate esters remaining constant
throughout the experiment,
indicating inability to degrade the
mononitrates.
Rhodococcus sp. strains SP2-4 and SP3-4.
Strain
SP2-4 exhibited a long lag period (12 h) before any growth on or
biodegradation of GTN (Fig. 2). However,
once biodegradation was initiated, GTN was rapidly converted to, first,
the dinitrates and then the mononitrates. Removal of the first nitrate
group from GTN was again nonspecific, with the ratio of 1,3-GDN to
1,2-GDN being approximately 1 to 2 during their accumulation. The
maximum concentration of 2-GMN was almost the same as that of its sole precursor 1,2-GDN, showing that the latter was converted mainly to the
2-GMN isomer. Significantly, this strain was capable of rapidly
biodegrading mononitrates, and hence, no nitrate esters were detected
in the growth medium at the end of the experiment.

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FIG. 2.
Biodegradation of GTN by Rhodococcus sp.
strain SP2-4. See the legend to Fig. 1 for key to symbols.
O.D.540, optical density at 540 nm.
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|
The growth and biodegradation profile of strain SP3-4 (data not shown)
was very similar to that observed for SP2-4 as expected,
since both
strains were found to belong to the genus
Rhodococcus.
There
was a long lag period before growth on and biodegradation
of GTN, but
once biodegradation was initiated, this strain completely
degraded GTN
via di-and mononitrate forms until no nitrate esters
could be detected
in the growth medium (Table
2). Strains SP2-4
and SP3-4 were probably
identical.
Klebsiella oxytoca strain SP2-5.
Of all the
strains tested, SP2-5 degraded GTN the most rapidly, with no GTN
detectable in the growth medium after 12 h. In contrast to the
other strains isolated, this strain produced greater quantities of
1,3-GDN than 1,2-GDN (ratio of 7 to 3). 1,3-GDN was incompletely
converted to 1-GMN, such that their concentrations at the end of the
experiment were approximately 40 µM and 150 µM, respectively (Table
2). The highest concentration of 1,2-GDN (at 12 h) was comparable
to the concentration of 2-GMN at the end of the experiment, indicating
that the conversion of 1,2-GDN to the mononitrate form was
regiospecific and exhibited a preference for the removal of the end
nitrate group. Throughout the experiment, the total concentration of
nitrate esters remained constant.
Arthrobacter ureafaciens SP1b-5.
Growth of strain
SP1b-5 on GTN as the sole source of nitrogen was extremely slow. GTN
was converted to 1,2-GDN and 1,3-GDN, like SP1a-2, in a ratio of
approximately 2 to 1 (Table 2). No mononitrates were detected during
the course of the experiment, and the total concentration of nitrate
esters remained constant.
 |
DISCUSSION |
Of the six isolates capable of utilizing GTN as their sole source
of nitrogen, two (SP1a-2 and SP1b-6) were identified as P. putida, two (SP2-4 and SP3-4) as Rhodococcus species,
one (SP1b-5) as an Arthrobacter species, and one (SP2-5) as
a Klebsiella species. When these four species are taken into
consideration alongside those strains already known to utilize GTN as a
sole nitrogen source, i.e., Agrobacterium radiobacter
(19), Enterobacter cloacae (3),
P. putida and Pseudomonas fluorescens
(4), it seems that the ability to biodegrade GTN is widely
distributed. The conversion of GTN to GDN has been shown to involve
/
barrel oxidoreductase flavoproteins (4, 7, 13),
which are related to old yellow enzyme (14). Such
oxidoreductase flavoproteins are a common family of enzymes, and hence
it is not surprising that the ability to biodegrade GTN may also be
widely distributed.
The pathway for the biodegradation of GTN, already established for
A. radiobacter (Fig. 3),
presents the possibility of regioselectivity in the removal of nitro
groups from either the central or one of the terminal carbons of GTN.
Of the four species isolated in this study, three (namely P. putida and the Rhodococcus and Arthrobacter species) produced 1,3-GDN and 1,2-GDN in the ratio of 1 to 2 which is
the ratio predicted for nonregiospecific removal of the first nitro
group from GTN. The P. putida strain isolated by Blehert et
al. (4) also exhibited a similar lack of regioselectivity. In contrast, the Klebsiella sp. strain SP2-5 isolated during
the present study produced 1,3-GDN and 1,2-GDN in a ratio of 7 to 3. Taking account of the twofold excess of terminal over central groups,
this corresponds to a 14 to 3 preference for central attack. In this
respect, the Klebsiella strain aligned itself with A. radiobacter (19), P. fluorescens
(4), and the fungus Geotrichum candidum
(5), all of which exhibited a distinct preference for the
removal of the central nitro group of GTN. On the other hand, one
fungus, Phanerochaete chrysosporium (11) has
been shown to possess a preference for the production of 1,2-GDN from GTN.

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FIG. 3.
Generalized pathway for the biodegradation of GTN
(adapted from reference 19 with permission from the
publisher) based on metabolite profiles for Agrobacterium
(19) and Pseudomonas sp. (4, 17)
and NAD(P)H dependence of GTN-degrading enzymes liberating
NO2 from GTN (4, 7, 13).
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|
In a similar manner, regioselectivity may also arise in the conversion
of 1,2-GDN (but not the symmetrical 1,3-isomer) to either 1-GMN or
2-GMN. For P. putida strain SP1a-2, GTN disappearance (and
thus production of GDNs) was complete after 18 h in culture; thus
analysis of the fate of 1,2-GDN in the post-18-h period was not
confounded by its continued formation. In the 18- to 60-h period,
1,2-GDN decreased by 67 µM (Fig. 1), and in the same period 2-GMN
increased by 53 µM, a conversion factor for 1,2-GDN to 2-GMN of 80%.
Similar calculations for P. putida strain SP1b-6 and
K. oxytoca strain SP2-5 gave conversion factors of 73 and
86%, respectively. Thus, these strains all showed a regioselectivity
of about 4 to 1 in favor of removal of the terminal nitro group in
1,2-GDN. For the Rhodococcus sp. strains SP2-4 and SP3-4,
similar calculations were not possible because both of the GMNs formed
were further degraded. Nevertheless, in both strains, the transient
maximum concentration of 2-GMN was similar to that of its sole
precursor 1,2-GDN, indicating again a strong preference for removal of
the terminal rather than the central nitro group. Thus, all of the strains isolated in this study, with the exception of SP1b-5 which produced neither GMN within the time scale of the experiments, exhibited a preference for the removal of the end nitro group from
1,2-GDN to produce 2-GMN. Such a preference has also been shown in
A. radiobacter (19) and P. chrysosporium (6, 11).
The predominance of terminal attack on 1,2-GDN contrasts with the
regioselectivity for attack on GTN (either central for K. oxytoca strain SP2-5 or nonselective for other strains). This suggests that different enzyme systems are involved in the degradation of GTN and 1,2-GDN, and this is supported, in turn, by the long lag
periods (6 to 12 h) between the onset of appearance of the GDNs
and that of the GMNs.
The most important and novel discovery from our experiments was that
complete biodegradation of GTN occurred in axenic cultures of the
Rhodococcus sp. strains SP2-4 and SP3-4. After a long lag period, both isolates achieved rapid biodegradation of GTN, including the removal of nitro groups not only from GTN and GDN but also from
GMN, thus attaining full denitration. Complete denitration of GTN has
previously been shown to occur only in mixed bacterial populations
(1, 15) or in cultures of Penicillium corylophilum Dierckx when grown in the presence of glucose and ammonium nitrate over long periods of time (>300 h) (20). Hence, to the
best of our knowledge, this is the first report of a single bacterial species that can achieve complete denitration of GTN and also utilize
its products as a sole source of nitrogen.
 |
ACKNOWLEDGMENTS |
We thank SRK Consulting and AECI Limited for providing soil
samples from wastewater soakaways; EXCHEM, Derbyshire, United Kingdom,
for supplies of GTN; the Royal Commission for the Exhibition of 1851 (London) for a Research Fellowship (S.J.M.); and the Royal Society
(London) for an equipment grant.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: School of
Biosciences, Cardiff University, Biomedical Building, Museum Ave., P.O.
Box 911, Cardiff CF10 3US, United Kingdom. Phone: 44 29 20876877. Fax:
44 29 20874116. E-mail: marshallsj1{at}cardiff.ac.uk.
 |
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Applied and Environmental Microbiology, June 2001, p. 2622-2626, Vol. 67, No. 6
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.6.2622-2626.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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