FEMS Microbiology Letters 119 (1994) 199-208 © 1994 Federation of European Microbiological Societies 0378-1097/94/$07.00 Published by Elsevier 199 FEMSLE 05992 Anaerobic degradation of halogenated benzoic acids by photoheterotrophic bacteria B.J. van der Woude and J.C. Gottschal *, M . d e B o e r , N . M . J . v a n d e r P u t , F . M . v a n d e r G e l d , R . A . P r i n s Department of Microbiology, University of Groningen, P.O. Box 14, 9750 AA Haren, the Netherlands (Received 2 March 1994; revision received and accepted 29 March 1994) Abstract: From light-exposed enrichment cultures containing benzoate and a mixture of chlorobenzoates, a pure culture was obtained able to grow with 3-chlorobenzoate (3-CBA) or 3-bromobenzoate (3-BrBA) as the sole growth substrate anaerobically in the light. The thus isolated organism is a photoheterotroph, designated isolate DCP3. It is preliminarily identified as a Rhodopseudomonas palustris strain. It differs from Rhodopseudomonas palustris WS17, the only other known photoheterotroph capable of using 3-CBA for growth, in its independence of benzoate for growth with 3-CBA and in its wider substrate range: if grown on 3-CBA, it can also use 2-CBA, 4-CBA or 3,5-CBA. Key words: Photoheterotrophy; Anaerobic dehalogenation; Rhodopseudomonas palustris; Benzoic acid; Bromobenzoic acid; Chlorobenzoic acid Introduction I n d u s t r i a l a n d a g r i c u l t u r a l activities a r e t h e main source of a great variety of halogenated c o m p o u n d s , m a n y o f which have a p p e a r e d to b e r e c a l c i t r a n t in m o s t e n v i r o n m e n t s . In spite o f t h e fact t h a t since t h e e a r l y seventies investigations have focussed on t h e c a p a c i t i e s o f a e r o b i c a n d a n a e r o b i c b a c t e r i a to d e g r a d e x e n o b i o t i c c o m p o u n d s [1,2], it is only r e c e n t l y t h a t p h o t o t r o p h i c m i n e r a l i z a t i o n o f s u b s t i t u t e d a r o m a t i c s has g a i n e d some attention. P h o t o h e t e r o t r o p h i c b a c t e r i a a r e k n o w n for * Corresponding author. Tel: (050) 632191; Fax: (050) 632154. SSDI 03 78-1097(94)00138-H t h e i r use o f a w i d e r a n g e o f substrates, e s p e c i a l l y if grown a n a e r o b i c a l l y in t h e light [3-8]. T h e m o s t obvious a d v a n t a g e s o f the t r a n s f o r m a t i o n o f x e n o b i o t i c c o m p o u n d s for p h o t o t r o p h i c b a c t e r i a w o u l d be: (1) detoxification; (2) t h e use as a s o u r c e o f C, S o r N; a n d (3) use as a sink for excess r e d u c i n g power. T h e p a r t i a l d e h a l o g e n a tion o f PCBs in t h e p r e s e n c e o f light a n d a c e t a t e was c l a i m e d to b e t h e result o f r e d u c t i v e d e h a l o g e n a t i o n by p h o t o t r o p h i c b a c t e r i a [9]. D i n i t r o p h e n o l e s c a n b e r e d u c t i v e l y t r a n s f o r m e d to m o n o n i t r o p h e n o l e s by p h o t o t r o p h i c b a c t e r i a [10]. T h e c o m p l e t e use o f 3 - c h l o r o b e n z o a t e ( 3 - C B A ) by Rhodopseudomonas palustris W S 1 7 [11] is dep e n d e n t on t h e p r e s e n c e o f b e n z o a t e . B e n z o a t e g r o w n cells o f t h e p h o t o t r o p h i c b a c t e r i u m H 4 5 - 2 , 200 similar to Rhodopseudomonas palustris, were able to photometabolize 3-CBA, but again did not utilize it as a sole growth substrate [12]. In this study we describe the enrichment and some properties of a phototrophic bacterium able to grow on 3-CBA as the sole carbon source anaerobically in light. Its characteristics are compared with those of Rhodopseudomonas palustrisa strain WS17. Materials and Methods Organisms For enrichments with halogenated benzoic acids, a mixture of samples collected from a ditch along a railway, a ditch near a polluted paint-factory site and De Biesbosch marsh sediment, all sites in the Netherlands, was used as an inoculum (50 g wet material/l). Sampling was done in sterile serum bottles which were completely filled with surface sediment and water. Rhodopseudomonas palustris strain WS17, able to metabolise 3-chlorobenzoate (3-CBA) in the presence of benzoate (BA) [11], was kindly supplied by Dr. Wyndham (Carleton University, Ottawa, Ontario, Canada). amide, 0.4 mg; pyridoxamine, 1.0 mg; pantothenic acid, 0.2 mg; cobalamin, 0.2 mg; biotin, 0.04 mg. Non-halogenated growth substrates and halogenated benzoic acids were added from separately autoclaved stock solutions. Enrichment cultures, 10 ml in closed 16-ml glass tubes, contained a mixture of mono- and dichlorinated benzoates (2-CBA, 3-CBA, 4-CBA, 2,3-CBA, 2,4-CBA, 2,5-CBA, 3,4-CBA and 3,5CBA: 0.2 mM each) or monobromobenzoates (2BrBA, 3-BrBA and 4-BrBA: 0.2 mM each). They were incubated without or in the presence of additional non-halogenated substrates: benzoate (1 mM), ethanol (3 mM) or decanoate (1 mM). In successive transfers of enrichment cultures, inhibition of algal growth was accomplished by the addition of 5 /xM 3(3,4-dichlorophenyl)l,l-dimethylurea (DCMU) from an ethanolic filtersterile 1 mM solution [13]. Cultures of R.palustris WS17 were kept viable by transfers in media containing BA (1 mM) and 3-CBA (1 mM). Cultures were checked for purity by streaking on Nutrient Broth (BBL, Cockeysville, USA) agar plates, which were incubated aerobically in the dark and anaerobically in the light, and by microscopic observation. Analytical procedures Growth media and enrichment Batch cultures were routinely incubated in the light at 30°C, pH = 7.0, in closed tubes or serum bottles, containing anaerobically prepared liquid medium and a N 2 gas phase. The low-chloride mineral salts medium contained the following components (per 1): MgSOa.7H20, 0.1 g; Ca(NOa)2.4H20 , 0.04 g; yeast extract, 0.1 g; EDTA, 1 mg; FeSO4.7H20, 2 mg; ZnSO4.7H20, 0.1 mg; MnC12.4H20, 0.03 mg; HaBO3, 0.3 mg; COC12.6H20, 0.2 mg; CUC1E.2H20, 0.01 mg; NiC1E.6H20 , 0.02 mg; Na2MoO4.2H20, 0.03 mg; Na2SeO3.5H20 0.026 mg; NaEWO4.2H20 0.033 mg. After autoclaving, the medium was completed by the addition of a K(NH4)PO 4 buffer, pH = 7.0, to a final concentration of 25 mM, and by adding a filter-sterile vitamin solution (values give final concentrations): para-aminobenzoic acid, 0.2 mg; folic acid, 0.1 mg; fatty acid, 0.1 mg; riboflavin, 0.2 mg; thiamin, 0.4 mg; nicotinic acid Chloride was measured colorimetrically according to the method of Bergman and Sanic [14] with NaCI as a standard. Benzoates were analyzed as described previously by Gerritse and Gottschal [15], with a lower detection limit of 0.01 mM. Growth was determined by measuring optical density at 660 nm. Dissolved or cell-carbon were analyzed with a total carbon analyzer as described by Gerritse et al. [16]. Absorption spectra of whole cells and of methanol-extracted pigments were made after the method by Yurkov and van Gemerden [17]. Chemicals All chemicals were of analytical grade. BA, 2-CBA, 3-CBA, 4-CBA and 2,4-CBA were purchased from Merck (Darmstadt, FRG). 2,3-CBA, 2,5-CBA, 3,4-CBA, 2-BrBA, 3-BrBA and 4-BrBA were from Aldrich (Gillingham, UK). 3,5-CBA was from Fluka (Buchs, Switzerland) 201 Results Enrichment of anaerobic phototrophic bacteria on chlorobenzoate and bromobenzoate Enrichment cultures were set up in the presence of a mixture of chloro- or bromobenzoates (see Material and Methods) either without an additional substrate or with benzoate, decanoate, or ethanol. After 2 months of anaerobic incubation in the light, tubes with BA or decanoate had turned reddish-brown. In BA-containing tubes, concentrations of 2-CBA and 3-CBA or 4-BrBA had decreased, and 4-BrBA and 3-BrBA had partly disappeared in tubes containing decanoate. Initial transfers from these cultures in fresh medium containing the CBA-mixture showed a decrease in concentration of 3-CBA only if BA (1 mM) was added. A decrease in 2-BrBA and 3BrBA was observed in subcultures containing the BrBA-mixture and BA. Subsequently, all CBAcontaining enrichment cultures were pooled and used to inoculate (10%) tubes containing a mixture of CBAs, with and without additional benzoate (BA, 1 mM). The same procedure was followed for BrBA cultures. In the subcultures, in the absence of BA, only poor growth of pigmented bacteria occurred, presumably at the expense of some yeast extract components, and no degradation of halogenated substrates was observed. However, if BA was present, CBAs containing subcultures turned red and showed complete disappearance of 3-CBA within 14 days. Disappearance was also observed for 3-BrBA in subcultures containing a mixture of BrBAs and BA. In anaerobic controls, autoclaved or incubated in the absence of light, no decrease of halogenated substrate concentrations was observed over a period of one month. After 3 successive transfers (1:10) in fresh medium containing 3-CBA (0.5 m M ) + BA (1 mM) the 3-CBA degrading culture appeared able to degrade 3-CBA or 3-BrBA without the addition of BA. The same was true for the 3-BrBA degrading culture. By anaerobic plating on 3-CBA in the light, a pure culture of a phototrophic bacterium, able to degrade 3-CBA as well as 3-BrBA, was obtained from the 3-CBA degrading mixed culture. The organism will be referred to as isolate DCP3. Identification of isolate DCP3 Isolate DCP3 is a motile, irregularly shaped rod (3 × 0.5 /~m) showing a budding type of cell division. Spectral analysis of whole cells cultured anaerobically in the light showed absorption maxima at 865, 806, 591, 384 nm (Bchla) and at 531, 499, 476 nm (carotenoids) [18]. In absorption spectra of methanol extracts these first two Bchla peaks shifted together to 770 nm, the third peak to 609 nm and the last peak to 364 nm. The three carotenoid peaks shifted to 509, 476 and 455 nm, respectively [17]. The red coloured cells contained lamellar arrangements of m e m b r a n e s (Fig. 1). Isolate DCP3 grew with acetate (/-/'max = 0.147 h - l ) , formate + CO2, thiosulphate + CO2, citrate, benzoate (/.t.max=0.066 h -1, Fig. 2A) or 4-hydroxybenzoate as sole carbon and electron sources anaerobically in the light. U n d e r aerobic conditions in the dark, yeast extract, acetate, pyruvate, citrate and 4-hydroxybenzoate can be used as sole carbon and energy sources, but not benzoate. On the basis of these characteristics, A Fig. 1. Transmission electron micrograph of a longitudinal section of isolate DCP3. It was embedded in Epon after fixation with 3% glutaraldehyde (1 h on ice) and post-fixation with osmium tetroxide and potassium bichromate. 202 8 1[ Ai" o,~,~ 1 to +, i/\ 1° ' ~ t/\ 1 +° o.01 ~ 0.o 1.6 -I-, , , , , , B :""""'N \ .-o-o--o ,, 0 (D ID --- %% oO.,<~ /so".: 1.0 :S E C 0 a L 0.1 o- \ ÷* ~~ ,4" o/ 8 ~. f/ ,,+'" @ O.E 0 0 0 ~ 0.0 0.01 C 1.8 ///0-0 1 A I C ~'.% % -+~Oao.1 / / U~ 0 g I l I I l l I i 0.01 0 1.0 l I l 1 50 :E vE 0.8 100 c e c o 0,0 160 time (h) Fig. 2. Growth of isolate DCP3 on (A) benzoate (BA), (B) 3-chlorobenzoate (3-CBA) or (C) 3-CBA added after growth with BA. OD660, ©; BA, e; 3-CBA, • CI-, +. 203 T h e d e c r e a s e in c o n c e n t r a t i o n s o f 2 - C B A o r 3 , 5 - D B A in m i x e d s u b s t r a t e c u l t u r e s in the prese n c e o f 3 - C B A c o n t i n u e d , slowly, after the d e p l e tion o f 3 - C B A (Fig. 3). This was a c c o m p a n i e d by s o m e i n c r e a s e in cell density. I n such m i x e d subs t r a t e cultures, 4 - C B A was n o t d e g r a d e d completely. U p o n r e n e w e d a d d i t i o n of 2 - C B A o r 3 , 5 - C B A a f t e r t h e i r c o m p l e t e d i s a p p e a r a n c e , furt h e r g r o w t h at t h e e x p e n s e o f t h e s e c o m p o u n d s was o b s e r v e d with t h e s a m e cell-yield as o b s e r v e d with 3-CBA alone. Yet, if fresh m e d i a c o n t a i n i n g 2- o r 3 , 5 - C B A w e r e i n o c u l a t e d ( 1 : 2 0 ) with thus p r e - g r o w n m a t e r i a l , no g r o w t h o c c u r r e d in t h e a b s e n c e o f 3-CBA. isolate D C P 3 c a n b e t e n t a t i v e l y i d e n t i f i e d as a Rhodopseudomonas palustris strain. Use of halogenated substrates by isolate DCP3 I s o l a t e D C P 3 was a b l e to grow o n meta substit u t e d c h l o r o - o r b r o m o b e n z o a t e as t h e sole carb o n s o u r c e with m a x i m u m specific g r o w t h r a t e s of 0.032 h - 1 a n d 0.023 h - 1 , r e s p e c t i v e l y (Fig. 2B, T a b l e 1). C u l t u r e s g r o w n on B A d e g r a d e d 3 - C B A within 2 h a f t e r its a d d i t i o n (Fig. 2C). N o g r o w t h was o b s e r v e d with any o f t h e o t h e r m o n o - or d i h a l o g e n a t e d b e n z o a t e s t e s t e d as sole substrates: 2 - C B A , 2 - B r B A , 4 - C B A , 4 - B r B A , 2,3C B A , 2,4-CBA, 2,5-CBA, 3,4-CBA, 3,5-CBA. If D C P 3 was g r o w n o n 3 - C B A in t h e p r e s e n c e o f o n e o f t h e s e h a l o g e n a t e d b e n z o a t e s only 2C B A , 4 - C B A o r 3 , 5 - d i c h l o r o b e n z o a t e (3,5-CBA) w e r e u s e d to s o m e extent. T h e c h l o r i n e r e c o v e r ies w e r e similar to t h o s e with 3 - C B A a l o n e (approx. 100%). A l s o t h e cell-yields ( c o r r e c t e d for growth on y e a s t extract a l o n e ) p e r s u b s t r a t e carb o n u s e d w e r e t h e s a m e as on 3 - C B A alone. This i n d i c a t e d t h a t 2 - C B A , 4 - C B A a n d 3,5-CBA, alt h o u g h n o t c o n s u m e d as sole s u b s t r a t e s by D C P 3 , w e r e d e h a l o g e n a t e d a n d c o m p l e t e l y u s e d for cell c a r b o n in t h e p r e s e n c e o f 3 - C B A ( T a b l e 1). A l s o c u l t u r e s grown on B A c o u l d use 2-CBA, b u t c u l t u r e s grown on a c e t a t e did not. Use of halogenated substrates by Rhodopseudomonas palustris strain WS17 S t r a i n W S 1 7 d e h a l o g e n a t e d 3 - C B A if grown on B A with s t o i c h i o m e t r i c c h l o r i n e r e l e a s e ( T a b l e 1), b u t n o t if grown on a c e t a t e (3 mM). C u l t u r e s g r o w n with 3 - C B A a n d B A s h o w e d i n c r e a s e d b i o m a s s a n d a similar cell-yield if c o m p a r e d with c u l t u r e s g r o w n on B A a l o n e ( T a b l e 1). A p a r t from 3 - C B A also 2-CBA, 2 - B r B A o r 3 - B r B A d i s a p p e a r e d in c u l t u r e s of W S - 1 7 grown on B A ( T a b l e 1). N o o t h e r m o n o - o r d i h a l o g e n a t e d b e n z o a t e s t e s t e d (see above) d e c r e a s e d in c o n c e n t r a t i o n within 14 days of i n c u b a t i o n . Table 1 Growth parameters of isolate DCP3 and Rhodopseudomonaspalustris WS17 with several substituted benzoates. Data are means of duplicates. BA, benzoate; CBA, chlorobenzoate; BrBA, bromobenzoate Substrate Isolate DCP3 p~ (h- 1) BA 2-CBA 3-CBA 0.066 0.032 4-CBA - 3,5-CBA 2-BrBA 3-BrBA 4-BrBA 0.023 - Strain WS 17 CIrecovery 1 (%) 92 99 106 96 Yield 2 (g/mol) Relative consumption (mM/mM) 79 75 79 n.a. 0.5 0.6 0.06 0 0.3 0.2 0 82 3 /z (h - I) 0.065 - CI recovery (%) 101 96 Yield (g/mol) 82 82 74 85 77 n.a.: not applicable. 1 C I - produced/substrate-bound chlorine disappeared. 2 mg cell-carbon produced/primary+ additional substrate (mM) disappeared. 3 CBA or BrBA consumption relative to BA consumption after 4 days of incubation in the presence of BA (1 mM). 204 oI ° - ' ° ' - ° ' - ° 0 1 "'~" 0.01 " ~t.O i '" "-- "~ " -" 0.0 B ~ 0...0--0---0~0 2.6 2.0 A E I: 1.6 0 @ @ :S E v 0 a 4~ 0.1 1.0 0 0 0.6 .++ b c @ o c 0 o \ 0.01 , 0.0 i C 2.6 ~0.---0--0 0 O''O--O''v, .'" Cj/ | ,+'''If" / k 0 @ @ v ~ 1.8 £ 0 1.0 C @ O C 0 0 II 0.1 0 0 0.8 0.01 0 100 time 200 0.0 800 (h) Fig. 3. Use of (A) 2-chlorobenzoate (2-CBA) (B) 4-chlorobenzoate (4-CBA) or (C) 3,5-dichlorobenzoate (3,5-CBA) by isolate DCP3 during and after growth on 3-CBA. Legends as in Fig. 2; 2-CBA, . 4-CBA, • 3,5-CBA, T. 205 1.0 0.8 00.0/0~0~0~0--0~0 A E c o (D cD X 0.1 I ¢3 O .' 0.4 c C 0.01 100 "+ c 0 '.~ 0 ?---- ..,;%_.,. --.,.. 0 "" 0.6 200 0.2 o o 0.0 3OO time (h) Fig. 4. Use of 3-CBA and 2-CBA by Rhodopseudomonas palustris strain WS17 during and after depletion of BA. The culture was inoculated with cells from an identical culture sampled after benzoate had been used completely.Legends as in Fig. 2; 2-CBA, *. In a culture of strain WS17 containing 2-CBA and 3-CBA, a continued slow decrease of 2-CBA and 3-CBA was observed after complete consumption of BA. This was even more apparent in a second transfer (Fig. 4), in which both 2-CBA and 3-CBA disappeared completely. Discussion From light-exposed enrichments with mixtures of chlorinated (CBA) or brominated (BrBA) benzoates, a phototrophic bacterium was isolated, able to use 3-chlorobenzoic acid (3-CBA) or 3bromobenzoic acid (3-BrBA) as a sole substrate for growth, anaerobically in the light. Based on its physiological and morphological properties, this isolate DCP3 is tentatively characterized as a strain of Rhodopseudomonas palustris [3,18]. This organism resembles Rhodopseudomonas palustris WS17, with the main difference being that strain WS17, in pure culture, is dependent on benzoate (BA) for growth on 3-CBA [11]. For several aerobic organisms it is known that xenobiotic substrates often fail to induce pathways leading to successful degradation and growth [19]. The initial dependence on BA of the subcultures from which DCP3 was isolated disappeared completely, either due to a shift in composition of the population or as a result of genetic changes in the initially enriched organism. Interestingly, the use of other chlorinated benzoic acids was not observed in the initial enrichment transfers. However, pure cultures of DCP3, grown on 3-CBA, also degraded 2-, 4-and 3,5CBA. Therefore the phototrophic isolate DCP3 appears to possess a dehalogenation mechanism relatively unspecific to the position of the substituent at the aromatic ring. This is in contrast with the capacities of most dehalogenating anaerobes isolated thus far [20,21]. As is the case with denitrifying organisms degrading halogenated BAs [22], the location of the dehalogenating step in the degradation route of DCP3 is unclear. Removal of the halogen substituent does not necessarily take place by initial dehalogenation, as observed in, for example, methanogenic systems [23] and during PCB dehalogenation by a phototrophic culture [9], but may also occur somewhere downstream the benzoate pathway. Reductive removal of a substituent in such a reductive ring-fission pathway has been shown for deamination of 4-aminobenzoyl-CoA to benzoyl-CoA in Desulfobacteriurn anilini [24]. The following observations reinforce the suggestion [11] that anaerobic dehalogenating phototrophs use a BA-inducible reductive ring-fission pathway [25]: (1) after the disappearance of BA, 3-CBA or 2-CBA were still slowly used by strain WS17; (2) isolate DCP3 can use 2-CBA not only if grown on 3-CBA but also if grown on BA; and (3) cultures of isolate DCP3 degraded 3-CBA without delay if pre-grown with BA. The lower growth rates of DCP3 with 3-CBA and 3-BrBA compared with BA may indicate that the halogen substituent impedes transport over the cell-membrane or perhaps one or more steps in this benzoate pathway proceed more slowly with the chlorine-substituted molecules than with the unsubstituted benzoate intermediates. So far the benzoate CoA-ligase is the only enzyme of the reductive ring-fission pathway studied. The purified enzyme of a R. palustris strain, not previously grown in the presence of chlorinated ben- 206 zoates, expressed only little activity for 3 - C B A (1%) a n d 2 - c h l o r o b e n z o a t e (10%) relative to B A [26]. Strains possessing d e h a l o g e n a t i n g capacities thus seem to have developed e n z y m e s with a wider substrate r a n g e for m e t a b o l i s m of halog e n a t e d b e n z o i c acids a n d higher specific activities for such c o m p o u n d s t h a n their n o n - d e h a l o g e n a t i n g relatives. T h e ecological i m p o r t a n c e of the d e c h l o r i n a t ing capacities of p h o t o t r o p h s is obscure. Estim a t e s c o n c e r n i n g the role of p h o t o t r o p h s in the t u r n o v e r of organic substrates in n a t u r a l systems are lacking [27]. T h e fact that the 3 - C B A m e t a b o lizing R. palustris WS17 has b e e n isolated from a n e n v i r o n m e n t with n o k n o w n history of pollution [11] suggests that, in m a n y a q u e o u s systems, the capacity exists for r a p i d acclimation to the use of h a l o g e n a t e d aromatics if a n a e r o b i c a n d light c o n d i t i o n s occur together. I n c o m b i n a t i o n with the results p r e s e n t e d above, this observation suggests that the role of p h o t o h e t e r o t r o p h i c bacteria in the removal of c h l o r i n a t e d aromatic comp o u n d s from c o n t a m i n a t e d e n v i r o n m e n t s may be m o r e i m p o r t a n t t h a n hitherto assumed. Acknowledgements W e t h a n k K.A. Sjollema for the p r e p a r a t i o n of the e l e c t r o n m i c r o g r a p h s a n d B.E.M. Schaub for technical assistance with p r e p a r a t i o n of the spectra. W e are grateful to Dr. T.A. 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