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System. Appl. Microbiol.

27, 653–660 (2004)


http://www.elsevier.de/syapm

Mycobacterium fluoranthenivorans sp. nov.,


a Fluoranthene and Aflatoxin B1 Degrading Bacterium
from Contaminated Soil of a Former Coal Gas Plant
D. Hormisch1,4, I. Brost2, G.-W. Kohring1, F. Giffhorn1, R. M. Kroppenstedt3, E. Stackebrandt3, P. Färber2, and
W. H. Holzapfel2
1
Saarland University, Applied Microbiology, Saarbruecken, Germany
2
Federal Research Center for Nutrition and Food, Institute of Hygiene and Toxicology, Karlsruhe, Germany
3
DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
4
LUFA – Landwirtschaftliche Untersuchungs- und Forschungsanstalt, Speyer, Germany

Received: May 21, 2004

Summary
Mycobacterium strain FA4T was isolated with fluoranthene as the single carbon source from soil of a for-
mer coal gas plant, polluted with polycyclic aromatic hydrocarbons. The physiological properties, fatty
acid pattern, and the 16S ribosomal RNA gene sequence indicated membership to the genus Mycobac-
terium, but were different from all type strains of Mycobacterium species. Based on comparative 16S
rRNA gene sequence analyses strain FA4T could be assigned to the Mycobacterium neoaurum taxon
showing 98% sequence similarity to M. diernhoferi as its closest neighbour. The occurrence of epoxymy-
colate in the cell wall differentiates FA4 from all members of this taxon which synthesize wax-ester my-
colates in addition to alpha-mycolates. Strain FA4T is able to degrade aflatoxin B1. This biological at-
tribute might be useful in biological detoxification processes of foods and feeds. From the investigated
characteristics it is concluded that strain FA4T represents a new species, for which we propose the name
Mycobacterium fluoranthenivorans sp. nov. The type strain of Mycobacterium fluoranthenivorans is
FA4T (DSM 44556T = CIP 108203T).

Key words: Mycobacterium fluoranthenivorans sp. nov. – polycyclic aromatic hydrocarbons – fluoran-
thene – aflatoxin B1 – degradation

Introduction
Among toxic waste product degrading bacteria, nu- grows with fluoranthene as the only carbon source, but
merous strains from the genera Rhodococcus and My- co-oxidizes other PAH’s during growth with fluoran-
cobacterium have been isolated from the environment thene.
and were described in detail [6, 7, 12, 13, 16, 27]. Some Aflatoxins with the naturally occurring subgroups B1,
of these organisms are able to degrade chlorinated com- B2, G1, G2, M1 and M2 are bisfurano-coumarin deriva-
pounds like vinyl chloride [11] and pentachlorophenol tives. They are structurally closely related to the above
[9], or compounds from the chemically diverse group of mentioned chemical compounds. Aflatoxins are pro-
polycyclic aromatic hydrocarbons (PAH’s) [2, 5, 12, 28, duced during the secondary metabolism of filamentous
34, 36]. These bacterial strains can either utilise a wide fungi. Especially aflatoxin B1 (AFB1) belongs to the most
variety of xenobiotics as growth substrates or they are re- dangerous naturally occurring mycotoxins because of its
stricted to only a few or a single hazardous compound. hepatotoxic, hepatocarcinogenic, mutagenic and terato-
Growth of Mycobacterium vanbaalenii [20], for example, genic effects, both on humans and on animals. AFB1 is
is described with naphthalene, phenanthrene, anthracene, produced both under moderate and under subtropic and
fluoranthene, pyrene, 1-nitropyrene, 3-methylcholan- tropic climatic conditions. Because of its hazardous nature,
thene, 6-nitrocrysene and benzo[a]pyrene. Mycobacteri-
um frederiksbergense [41] mineralises phenanthrene, flu-
oranthene or pyrene and Mycobacterium hodleri [21] Genbank accession number: AJ617741

0723-2020/04/27/06-653 $ 30.00/0
654 D. Hormisch et al.

different physical and physico-chemical techniques have samples of the heptamethylnonane phase 1:350 with methanol
been developed to detoxify and to degrade AFB1 [40]. prior to injection.
AFB1 is a physically and physico-chemically stable
molecule, e.g. temperatures > 250 °C are necessary for ef- Analytical methods
As described [37], 40 mg wet weight of cells were saponified,
fective destruction. Foods treated for physical degrada- methylated and extracted. The derived fatty acid methyl esters
tion of AFB1 are not acceptable for human consumption. (FAMEs) were analysed by GC (model 5898A, Hewlett Packard,
Therefore, biological degradation of AFB1 without sig- controlled by MIS software, Microbial ID) and the “Microbial
nificant alteration of the sensory characteristics of a Identification” standard software package [35]. Thin layer chro-
food, would be most advantageous, particularly in situa- matography investigation of mycolic acids followed described
tions of food scarcity. During the search for bacterial de- methods [24, 26]. Mycolic acids were extracted from saponified
graders of AFB1, strains from different habitats, includ- cells and transferred to their bromophenacyl esters [3, 25]. After
ing soils from a former coal gas plant, were screened for addition of low and high molecular mass standards (Ribi Im-
their ability to degrade AFB1. Among the few positive munoChem Research) the mixture was separated and analysed
by HPLC (C18 Ultrasphere XL cartridge column, 35 °C,
strains, one was found to belong to the genus Mycobac- Hewlett Packard Series 1050 operated with the Sherlock System
terium but could not be allocated to any known species software, MIDI Inc.). For the analysis of the mycolic acid cleav-
of this genus, thus representing a putative new species. age products (MACP) the cells were treated as described above
This paper describes Mycobacterium strain FA4T which for fatty acids. To enhance the pyrolysis of the mycolic acids 10
is able to degrade AFB1 most effectively. µl of 0.2 M methanolic TMSH was added to the fatty acid/my-
colic acid methyl esters extract and analysed by GC [29].

Material and Methods 16S rRNA gene sequence determination


Extraction of the DNA, PCR-mediated amplification of the
16S rDNA and purification of the PCR products were done as
Isolation
described [33]. The purified amplificates were analysed with an
PAH polluted soils from a former coal gas plant in Saar-
Applied Biosystems 373A DNA Sequencer. The 16S rRNA gene
bruecken-Burbach, Germany, were screened for potential PAH
sequence was aligned manually with published sequences from
degraders; in this process, strain FA4T was isolated by the fol-
representatives of the actinomycete sublines of descent included
lowing procedure: The sampling comprised 3 g of soil which
in the DSMZ database of sequences. Neighbour joining analysis
were added to 25 ml of liquid medium containing in 1000 ml
and calculation of bootstrap values were done according to the
H2O: 0.9 g KH2PO4, 2.5 g Na2HPO4· H2O, 0.2 g MgCl2· H2O,
PHYLIP program [8].
0.5 g KNO3, 0.1 g (NH4)2SO4, 0.2 g NH4Cl, 3.59 mg
CaCl2· H2O, 1.66 mg FeCl3· H2O, 10 ml SL4 [30], and 10 ml of
AFB1 degradation experiments
vitamin solution [31], adjusted to a final pH of 7.2. As a carbon
The method for the quantitative determination of AFB1 is
source 2.5 ml of fluoranthene (10 mg/ml) dissolved in hep-
based on the CEN/DIN method prEN 14123 (“Foodstuffs – De-
tamethylnonane (ICN Biochemicals) were loaded on top of the
termination of aflatoxin B1 and the sum of aflatoxin B1, B2, G1
medium, which provided the organisms with a constant concen-
and G2 in peanuts, pistachios, figs and paprika powder”). Sim-
tration of fluoranthene in the water phase, determined by the
plification was possible by using a miniaturised in vitro test sys-
partition coefficient. The cultures were incubated at 28 °C on a
tem, whereby there was no need for the use of an immuno-affin-
rotary shaker. After visible growth, the enrichment cultures were
ity column clean-up of the test samples. In contrast to complex
transferred to fresh media for at least three times and then sepa-
foodstuff like peanuts, pistachios or maize, which are rich in
rated on R2A agar plates (Difco Lab.). Single colonies were
protein and fat/oil, the complete medium used in these tests did
grown again in the described liquid medium and finally tested
not require a clean-up of samples. The test cultures of strain FA4
for purity on R2A agar plates.
have been regularly subcultured on an AFB1-containing medium
at least three times for 12 hours at 30 °C for a possible induc-
Characterisation and biochemical tests
tion of enzymes involved in AFB1 degradation. Media used for
All tests followed methods indicated [41] and were per-
the precultivation of the cells and used in the degradation exper-
formed in duplicate. As a control, all tests were also carried out
iments itself, were supplemented with AFB1 to an initial concen-
with M. hodleri which exhibited the same results as reported in
tration of 2.5 ppm. The degradation experiments were per-
the literature [21]. Morphological analysis, Gram staining and
formed on a rotary shaker at 30 °C in the dark. Samples for
acid-alcohol fastness were investigated by phase contrast and
analysis of the AFB1 concentration were withdrawn at 12 h, 36
bright field microscopy. The ability to grow at different temper-
h and 72 h after inoculation. The remaining AFB1 concentration
atures, pigment production and photoreactivity were deter-
was quantitatively determined by HPLC (stationary phase:
mined after 2 weeks of growth in Middelbrook medium [23].
LiChroCart 250-4 Hypersil ODS [5 µm] [MERCK, Germany];
Tests for urease [10], catalase [22] and nitrate reductase activity
mobile phase: CH3CN:CH3O:H2O [25: 25 :50/vol:vol:vol];
or Tween 80 hydrolysis [1] were performed as described in the
detection: DAD at 365 nm).
citations. Growth investigations with sugars and sugar alcohols
[40], and other physiological tests were performed as described
[19, 41].
Growth with different PAH’s as single carbon sources was in- Results and Discussion
vestigated in the same medium described under “isolation”, sup-
plemented with 10% (w/v) of each PAH dissolved in hep- Morphological and physiological properties
tamethylnonane (10 mg/ml). Degradation of the PAH’s was de-
termined by reverse phase HPLC (Nucleosil 120-5-C-18 col- The organism FA4T was rod shaped (2 µm length,
umn, 48.5% methanol and 3% acetic acid in water as the mo- 1 µm diameter), Gram-positive, acid-alcohol-fast and not
bile phase, UV detection, Beckman System Gold) after diluting motile. The strain was nonchromogenic and grew at
Mycobacterium fluoranthenivorans sp. nov. 655

Table 1. Physiological properties of M. fluoranthenivorans DSM 44556T, M. diernhoferi, M. hodleri and M. vanbaalenii.

Mycobacterium Mycobacterium Mycobacterium Mycobacterium


diernhoferi d fluoranthenivorans hodleri d vanbaalenii e

Formation of pigment a N N S S
Gram stain + + + +
Acid fast stain + + + +
Growth at 20 °C/28 °C/37 °C + + + +
Growth at 42 °C – – – –
Tween 80 hydrolysis – – – (+) c +
Nitrate reduction + – – +
Urease activity n.a. – +c +
Catalase activity – + + +
Growth on:
Xylose + + + –
Trehalose – + + (–) c –
Sorbitol – + + –
Utilisation b of:
N-acetyl-d-glucoseamine – + + n.a.
D-Glucosaminic acid – + – n.a.
Gluconate + + + n.a.
D-Sucrose – + – –
D-Turanose – + – n.a.
L-Rhamnose – + + –
D-Ribose – + + n.a.
D-Arabitol – + + n.a.
I-Inositol + + + n.a.
Mannitol + + + n.a.
Citrate – + – –
2-Oxoglutarate + + + n.a.
Glutarate n.a. + – n.a.
Succinate – + + n.a.
L-Alanine + + + n.a.
L-Aspartate – + + n.a.
L-Leucine + + + n.a.
L-Proline + + + n.a.
L-Valine – + + n.a.
Putrescine + + + n.a.
Acetamide – + – n.a.
Phenyl acetic acid – + – n.a.
Benzoate – + – n.a.
4-Amino-benzoate – + – n.a.
4-Hydroxy-benzoate – + – n.a.
Quinate – + + n.a.
P-nitrophenylphosphoryl-choline + + – n.a.
a
S, scotochromogenic, N, nonchromogenic.
b
Assimilation of auxanographic substrates was detected photometrically by means of reduction of the redox dye MTT (Kirchhof
et al. 1992). + = E540(test) – E540 (control) > 0.129; – = E540 (test) – E540 (control) <0.129.
c
Data from Kleespies et al. [21], d Data from Willumsen et al. [41], e Data from Khan et al. [20] n.a. data not available

20 °C, 28 °C and 37 °C but not at 42 °C. In contrast to a tives and p-nitrophenylphosphoryl-choline were utilised
well expressed catalase activity, no urease or nitrate re- as aromatic substrates (Table 1).
duction activity was observed, and Tween 80 was not hy- Table 1 summarises the physiological characteristics of
drolysed (Table 1). strain FA4T, including its utilisation of a broad spectrum
From the group of polycyclic aromatic hydrocarbons, of carbon sources such as sugars, sugar alcohols, amino
only the isolation substrate fluoranthene was metabolised acids, organic acids and mono aromatic compounds.
by strain FA4T. No growth was detected with naphtha-
lene, anthracene, phenanthrene, acenaphthene, acenaph-
Degradation of AFB1
thylene, fluorene, chrysene, or pyrene as the single carbon
source (Table 2), and the strain could not utilise biphenyl. AFB1 degradation by Mycobacterium strain FA4 was
However, phenylacetic acid, benzoate, benzoate deriva- relatively rapid and effective, leaving no detectable AFB1
656 D. Hormisch et al.

Table 2. Growth of M. fluoranthenivorans DSM 44556 T, M. hodleri, M. vanbaalenii and M. frederiksbergense with biphenyl or sev-
eral polycyclic aromatic hydrocarbons as single carbon sources.

Mycobacterium Mycobacterium Mycobacterium Mycobacterium


fluoranthenivorans hodleri a vanbaalenii b frederiksbergense c

Biphenyl – n.a. + n.a.


Naphthalene – n.a. + n.a.
Anthracene – – + –
Phenanthrene – – + +
Acenaphthene – n.a. n.a. n.a.
Acenaphthylene – n.a. n.a. n.a.
Fluorene – – n.a. –
Fluoranthene + + + +
Chrysene – n.a. n.a. n.a.
Pyrene – – + +
a
Data from Kleespies et al. [21], b Data from Khan et al. [20], c Data from Willumsen et al. [41] n.a. data not available

Table 3. Composition of FAMEs derived from whole-cell hydrolysates of strain FA4T and members of the Mycobacterium neoaurum
cluster.

Fatty acid (%) FA4T DSM 43524T DSM 44346T DSM 44077T DSM 44183T DSM 44074T

10:0 0.66 – – – – –
12:0 0.60 – – – – –
14:0 10.02 6.23 5.45 4.73 5.74 5.72
15:0 – – 0.66 0.35 1.05 –
16:1 cis-7 – 2.17 6.30 0.54 1.49 3.48
16:1cis-9 13.46 0.77 – 0.83 2.42 5.23
16:1cis-10 4.60 5.65 3.41 3.56 6.07 –
16:0 42.11 25.27 31.44 26.87 25.17 28.31
16:0 10-methyl 2.17 – – – 0.76 –
17:0 – – – 0.42 – –
18:2 – – – 0.45 0.63 –
18:1cis-9 16.80 20.57 34.83 14.55 20.27 30.46
18:0 3.37 3.98 2.27 3.00 1.24 1.96
18:0 10-methyl 5.09 11.15 1.36 9.33 18.46 5.57
20:0 1.11 – 1.36 0.46 – –
18:0 alcohol – 18.00 10.78 16.77 13.93 15.07
20:0 alcohol – 4.57 1.71 16.32 2.77 1.74

Values are percentages of total fatty acids. Secondary alcohols that are released from wax esters are included. Examples of abbrevia-
tions: 16:0, hexadecanoic acid (palmitic acid);
18:1 cis-9, cis-9-octadecenoic acid (oleic acid); 18:0 10 methyl, 10-methyloctadecanoic acid (tuberculostearic acid); 20: 0 alcohol, 2-
eicosanol.
M. chitae DSM 43633, M. farcinogenes DSM 43637, M. fortuitum DSM 46621, M. peregrinum DSM 43271, M. porcinum DSM
44242, M. senegalensis DSM 43656, M. smegmatis DSM 43756.

after 72 h. The AFB1 concentration was reduced to dition (Table 3). The pyrolysis esters of the mycolic acids
amounts of 70% to 80% of the initial concentration showed a chain length of 22, 24 and 26 carbon atoms
within 36 hours. In further experiments, cell-free extracts (Table 4). The mycolic acid pattern separated by TLC
of Mycobacterium FA4 have been used in the same way, was composed of alpha-mycolates and epoxy mycolates
both to confirm these observations and the enzymatic na- (Table 4). Analyses of mycolic acids by HPLC revealed a
ture of the degradation activity (data not shown). characteristic UV-HPLC chromatogram with a two-peak
cluster that emerged late and close together after 6–8
minutes (Fig. 1). It seems that there is a correlation be-
Chemotaxonomic properties
tween this HPLC-chromatogram and the occurrence of
The analysis of the fatty acids revealed a pattern com- alpha-mycolate and epoxy-mycolates because this two-
posed of straight chain saturated and unsaturated fatty peak cluster is always present in mycobacteria species
acids with an even number of carbon atoms. The diag- which synthesise alpha-mycolates and epoxy-mycolates
nostic 10-methyl branched fatty acids were found in ad- i.e. M. agri, M. chelonae, M. chitae, M. farcinogenes,
Mycobacterium fluoranthenivorans sp. nov. 657

Table 4. Mycolic acids and pyrolysis esters of strain FA4T and members of the M. neoaurum group a.

Mycolic acidsa FA4T DSM 43524T DSM 44346T DSM 44077T DSM 44183T DSM 44074T

alpha-mycolates + + + + + +
alpha′-mycolates (+) – – – – –
Methoxy-mycolates – – – – – –
Keto-mycolates – + + + + +
Epoxy-mycolates + – – – – –
Waxester-mycolates – + + + + +
w-1-Methoxy-mycolates – – – – – –
Pyrolysis esters
C22: 0 + + + n.d. + +
C24: 0 + + – n.d. + –
C26: 0 + – – n.d. – –
a
Data from Willumsen et al., 2001; b +, present; –, absent; (+), small amounts present; n.d., no data.
M. diernhoferi DSM 43524T, M. frederiksbergense DSM 44346 T, M. gadium DSM 44077 T, M. hodleri DSM 44183T, M. neoaurum
DSM 44074T.

Fig. 1. Mycolic acid HPLC


elution profile of FA4T
(= DSM 44556T). LIS, low-
molecular-mass internal stan-
dard; HIS, high-molecular-
mass internal standard.

members of the M. fortuitum., M. goodie, M. pere- scribed species was M. diernhoferi ATCC 25795T (98%
grinum, M. smegmatis, M. wolinskyi, M. porcinum and sequence similarity). Strain ATCC BAA-823, proposed as
M. senegalense [4, 15]. “Mycobacterium hackensackense” [17] (AY266138)
shows identity with the homologous sequence of strain
FA4T.
Phylogenetic analysis
Determination of the 16S rRNA gene sequence and the
Differentiation of strain FA4T from other mycobacteria
comparison with other sequences of members of the
genus Mycobacterium revealed that strain FA4T belongs Strain FA4T could clearly be separated from the other
to M. neoaurum subgroup of fast-growing mycobacteria. members of the M. neoaurum complex by its fatty acid
The closest relationship obtained with the type of a de- pattern. FA4T lacks the two secondary alcohols C18:0
658 D. Hormisch et al.

Table 5. Mycolic acids of Mycobacterium sp. FA4T and other species showing alpha- and epoxy-mycolates in their mycolic acid pat-
terns.

DSM 43633T

DSM 43637T

DSM 46621T

DSM 43271T

DSM 44242T

DSM 43656T

DSM 43756T
Mycolic acids a

FA4T
alpha-mycolates + + + + + + + +
alpha′-mycolates (+) + (+) + (+) + (+) +
methoxy-mycolates – – – – – – – –
keto-mycolates – – – – – – – –
epoxy-mycolates + + + + + + + +
waxester-mycolates – – – – – – – –
omega-1-methoxy-mycolates – – – (+) (+) (+) (+) –
a
Data from Vincent Levy-Frebault & Portales, 1992; Hinrikson & Pfyffer, 1994.
M. chitae DSM 43633T, M. farcinogenes DSM 43637 T, M. fortuitum DSM 46621T, M. peregrinum DSM 43271T,
M. porcinum DSM 44242 T, M. senegalensis DSM 43656 T, M. smegmatis DSM 43756 T.

Fig. 3. AFB1 degradation by viable cells of Nocardia corynebac-


terioides DSM 44601 (former Flavobacterium aurantiacum,
DSM 12676) and Nocardia corynebacterioides DSM 20151 in
comparison to Mycobacterium fluoranthenivorans DSM 44556T
(FA4T). All strains were cultivated in Standard I medium con-
taining 2.5 ppm AFB1, at 30 °C under shaking conditions for
12 h, 36 h and 72 h.

Fig. 2. Dendrogram of 16S rRNA gene sequence relatedness


showing the phylogenetic position of strain DSM 44556 T within waxester mycolates instead of epoxy-mycolates are found
the radiation of some fast growing species of the genus My- in addition to alpha-mycolates which are present in all
cobacterium. Numbers at branching points refer to bootstrap mycobacteria [15, 41].
values (500 re-samplings). Scale bar, 5 inferred nucleotide sub-
In combination, the results of this investigation
stitutions per 100 nucleotides.
demonstrate that the described strain FA4T represents a
new species of the genus Mycobacterium. Compared to
other PAH metabolising mycobacteria, there are pro-
and C20:0 which are always present in members of the found differences to bacteria with a broad PAH substrate
M. neoaurum complex. This taxon includes M. diern- spectrum such as M. frederiksbergense or M. vanbaalenii
hoferi, M. frederiksbergense, M. gadium, M. hodleri and (Table 2). M. hodleri, which could also only use fluoran-
M. neoaurum [32, 41]. Instead of the secondary alcohols thene, exhibited many differences in the physiological
a C26:0 mycolic acid pyrolysis ester is found in the ex- data as shown in Table 1. In contrast to M. fluoran-
tract of FA4T. This ester is missing in the other species of thenivorans sp. nov., M. hodleri was scotochromogenic,
this taxon (Table 3). FA4T synthesized alpha-mycolates expressed urease activity and could not utilise most of the
and epoxymycolates. This mycolic acid pattern is shared mono aromatic substrates. The strain with the highest
by M. chitae, M. farcinogenes, M. fortuitum, M. pere- similarity with respect to 16S rRNA gene sequence analy-
grinum, M. porcinum, M. senegalense and M. smegmatis sis, M. diernhoferi, expressed also significant differences
[15] (Table 5) which are not related to FA4T by 16S rRNA in the utilisation of sugars, some amino acids and the
gene sequences. In members of the M. neoaurum complex mono aromatic compounds (Table 1).
Mycobacterium fluoranthenivorans sp. nov. 659

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30. Pfennig, N.: Anreicherungskulturen fuer rote und gruene Tel.: ++(0)721-6625-450; Fax: ++(0)721-6625-453;
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