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Papillibacter Cinnamivorans Gen. Nov., Sp. Nov., a Cinnamate-Transforming Bacterium from a Shea Cake Digester

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Papillibacter Cinnamivorans Gen. Nov., Sp. Nov., a Cinnamate-Transforming Bacterium from a Shea Cake Digester International Journal of Systematic and Evolutionary Microbiology (2000), 50, 1221–1228 Printed in Great Britain Papillibacter cinnamivorans gen. nov., sp. nov., a cinnamate-transforming bacterium from a shea cake digester S. Defnoun,1,2 M. Labat,1 M. Ambrosio,2 J.-L. Garcia and B. K. C. Patel3 Author for correspondence: B. K. C. Patel. Tel: j61 417 726671. Fax: j61 7 38757800. e-mail: bharat!genomes.sci.gu.edu.au 1 Laboratoire IRD de A new, strictly anaerobic, Gram-positive, non-sporulating, mesophilic Microbiologie, Universite! bacterium, designated strain CIN1T (Tltype strain) was isolated from an de Provence – CESB/ESIL – Case 925, 163 Avenue de anaerobic digester fed with shea cake rich in tannins and aromatic compounds. Luminy, 13288 Marseille Cells of strain CIN1T were rod-shaped, had characteristically pointed ends Cedex 9, France (13–30i05–06 µm) and occurred singly, in pairs and sometimes in chains of 2 Laboratoire Chimie et up to six. The pH range for growth was 69–85 and the temperature growth Environnement, Universite! range was 15–40 SC. Optimum growth occurred with yeast extract and de Provence, 3 Place Victor Hugo, 13331 Marseille, cinnamate at 37 SC and a pH of 75. The isolate transformed cinnamate by Cedex 3, France degrading the aliphatic side chain to produce acetate and benzoate rather than 3 School of Biomolecular by aromatic ring cleavage or demethoxylation. The position of the methoxyl and Biomedical Sciences, group appears to be important in the degradation of the aliphatic side chain of Faculty of Science, Griffith cinnamate; consequently, 3-methoxycinnamate and 4-methoxycinnamate, but University, Brisbane, Queensland 4111, not 2-methoxycinnamate, are transformed to produce acetate and Australia methoxybenzoates, namely 3-methoxybenzoate and 4-methoxybenzoate, respectively. Crotonate is degraded to acetate and butyrate. The GMC content of the DNA is 56 mol%. Phylogenetic analysis of the 16S rRNA gene of strain CIN1T indicated that it was a member of the low-GMC-containing Gram-positive branch with a specific relationship to Sporobacter termitidis (sequence identity of 88%). The phylogenetic results concur with the phenotypic data which reveals that the isolate is a novel bacterium and, based on these findings, strain CIN1T (lDSM 12816TlATCC 700879T) has been designated Papillibacter cinnamivorans gen. nov., sp. nov. Keywords: Papillibacter cinnamivorans, anaerobes, aromatic compounds, transformation, cinnamate INTRODUCTION member of the low-GjC-containing Gram-positive branch, Pelobacter acidigallici (Schink & Pfennig, Lignin is the second most abundant natural product 1982) and Pelobacter massiliensis (Schnell et al., 1991), on earth and consists of a vast array of aromatic members of the Proteobacteria, which de-aromatize monomers including cinnamate (Collberg, 1988; Healy aromatic compounds such as gallate, resorcinol and & Young, 1979; Healy et al., 1980). It is now well phloroglucinol to produce acetate, Holophaga foetida established that monoaromatic compounds are at- (Liesack et al., 1994), a member of the Proteobacteria, tacked by a phylogenetically diverse range of anaerobic and Sporobacter termitidis (Grech-Mora et al., 1996), a micro-organisms, some of which completely ferment member of the low-GjC-containing Gram-positive the aromatic compounds and others that are only branch, are unusual in that they first transfer the ether- involved in transformation of such compounds. Pure linked methyl groups to sulfide-producing methane- cultures with the ability to ferment aromatic com- thiol or dimethylsulfide followed by de-aromatization pounds include Coprococcus sp. (Patel et al., 1981), a of the aromatic ring structure. Until recently, mono- hydroxylated aromatic compounds were considered ................................................................................................................................................. undegradable by anaerobes, but recently Sporoto- The GenBank accession number for the 16S rDNA sequence of strain CIN1T maculum hydroxybenzoicum (Brauman et al., 1998), a is AF167711. member of the low-GjC-containing Gram-positive 01317 # 2000 IUMS 1221 S. Defnoun and others branch, has been shown to degrade 3-hydroxybenzoate 0n5% Biotrypcase; strain CIN1T failed to grow under these via the benzoyl-CoA pathway subsequent to the conditions. removal of the hydroxyl group. In other cases, de- Light microscopy and electron microscopy. Light and elec- aromatization of the ring requires syntrophic co- tron microscopy were performed as described previously culture, as is the case with Syntrophus buswellii strain (Fardeau et al., 1997). GA, a member of the Gram-negative Proteobacteria Growth studies. Substrates were added from sterile an- that degrades cinnamate under anaerobic syntrophic aerobic stock solutions. All growth studies were conducted conditions only (Auburger & Winter, 1995). The in duplicate unless otherwise indicated. The isolate was anaerobic members of Proteobacteria which transform subcultured at least twice under the same experimental conditions. Growth studies were performed in basal medium aromatic compounds with ring cleavage include photo- −" synthetic bacteria (some strains of Rhodopseudomonas containing 5 mM cinnamate and 0n5 g yeast extract l . For palustris) (Harwood & Gibson, 1988), sulfate-reducing pH studies, the medium was adjusted to the required pH by bacteria (Desulfobacterium and Desulfococcus), metal- injecting appropriate volumes from anaerobically prepared reducing bacteria (Geobacter) and denitrifying bacteria stock solutions of 1 M HCl, 10% NaHCO$ and 8% Na#CO$. Temperature range for growth was determined (Thauera). between 10 and 55 mC using the basal medium adjusted to In this paper, the isolation and characterization of a the optimum pH. For studies on NaCl requirements, NaCl new anaerobic bacterium, which transforms a limited was weighed directly in the tubes to give the required range of aromatic compounds, namely cinnamate, 3- concentration. For concentrations lower than 1%, different aliquots of 10% (w\v) NaCl were injected into predispensed methoxycinnamate and 4-methoxycinnamate, without basal medium to give the required concentration. de-aromatization of the ring are described. Physio- logical studies including metabolism of the substrates Sporulation test. Cells from various stages of the growth and end-products are reported. phase and from cultures grown on different substrates were observed microscopically for the presence of spores. In addition, the culture was tested for heat resistance. For this, METHODS cells grown in basal medium containing 5 mM cinnamate T were heated for 10 min at temperatures of 80, 90 and 100 mC. Source of strains. Strain CIN1 was isolated from an The cells were cooled quickly to ambient temperature, anaerobic digester fed with shea cake situated in Burkina inoculated into fresh cinnamate-containing basal medium Faso (Africa). The digester had previously been inoculated and growth was checked after at least 1 week incubation at with anaerobic sludge from the pit of a slaughterhouse. 37 mC. Carbon and energy sources were composed exclusively of tannins and aromatic compounds. Substrate utilization studies. For substrate utilization studies, the isolate was subcultured at least once under the Culture media. A basal medium described below was used same experimental conditions. Substrate utilization studies for enrichment, isolation and routine cultivation. The were performed in basal medium amended with one of the medium was prepared using the anaerobic technique de- following substrates to give a final concentration as indi- scribed by Hungate (1969) and modified for use with syringes cated: 5 mM for all aromatic compounds including mono- (Macy et al., 1972; Miller & Wolin, 1974). The basal medium methoxylated aromatic compounds (2-, 3-, 4-methoxy- −" contained (l deionized water): 0n2gK#HPO%; 1 g NaCl; cinnamate), di-methoxylated aromatic compounds (2,3-, 0n15 g CaCl#;2H#O; 0n4 g MgCl#;6H#O; 0n5 g KCl; 0n5g 2,4-, 2,5-, 2,6-, 3,5-dimethoxybenzoate, 3,5-dimethoxy- cysteine–HCl; 0n5 g yeast extract; 1n5 ml trace element cinnamaldehyde), tri-methoxylated aromatic compounds solution (Widdel & Pfennig, 1981); and 1 mg resazurin. The (3,4,5-trimethoxybenzoate, 3,4,5-trimethoxycinnamate, pH was adjusted to 7n0 with a 10 M NaOH solution. The 3,4,5-trimethoxyphenylacetate, 3,4,5-trimethoxyphenyl- medium was then boiled under a stream of O#-free N# gas propionate), hydroxy-methoxylated aromatic compounds and cooled to room temperature. Unless otherwise indi- (ferulate, syringate and sinapate), mono-hydroxylated aro- cated, 5 ml aliquots were dispensed into Hungate tubes matic compounds (2-, 3-, 4- hydroxycinnamate, phenol and under N#–CO# (80:2) gas mixture and subsequently ster- 4-hydroxybenzoate), polyhydroxylated aromatic com- ilized by autoclaving at 110 mC for 45 min. Prior to use, pounds (caffeate, gallate, tyrosol, phloroglucinol, pyrogal- 0n2ml 5% (w\v) NaHCO$ and 0n05 ml 2% (w\v) lol, catechol and hydroquinone), non-hydroxylated Na#S;9H#O were injected from anaerobic sterile stock and non-methoxylated substituted cinnamyl derivatives solutions into the pre-sterilized basal medium. (α-methylcinnamate, methyl trans-cinnamate, cinnamyl alcohol, trans-cinnamate methyl ester and coumarine) and Enrichment and isolation. The liquid digester sample (0n5 ml) was inoculated into the basal medium emended with 5 mM non-substituted aromatic compounds (cinnamate, benzoate, hydrocinnamate and phenylacetate); 10 mM for
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