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1 Laboratory of Microbiology of Anthropogenic Environments, Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
2 Subdepartment of Environmental Technology, Wageningen University, Wageningen, The Netherlands
3 Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
Correspondence
Sofia N. Parshina
sonjaparshina{at}mail.ru
| ABSTRACT |
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Electron micrographs of Soehngenia saccharolytica BOR-YT (Fig. I) and Clostridium amygdalinum BR-10T (Fig. II) are available in IJSEM Online.
| INTRODUCTION |
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Clostridium aceticum oxidized aromatic aldehydes (Lux & Drake, 1992
). A few Desulfovibrio strains oxidized the aldehyde group of vanillin and other aromatic aldehydes with sulfate as an electron acceptor (Zellner et al., 1990
). A limited number of the strains were tested for their ability to convert benzaldehyde. Clostridium acetobutylicum reduced benzaldehyde, but 10 mM benzaldehyde caused inhibition of growth. This bacterium required the presence of glucose and butyrate in the medium (Green et al., 1994
). Desulfovibrio desulfuricans both oxidized and reduced benzaldehyde in the presence of nitrate (Parekh et al., 1996
).
In a previous study (Parshina et al., 2000
), the isolation of two bacterial strains able to convert benzaldehyde in the absence of inorganic electron acceptors was described. The bacteria were isolated from an anaerobic upflow anaerobic sludge bed (UASB)-reactor treating potato starch waste water. One bacterium (strain BOR-YT) performs the dismutation of benzaldehyde to benzoate and benzylalcohol. The other bacterium (strain BR-10T) uses benzaldehyde as an electron acceptor resulting in the formation of benzylalcohol and obtains metabolic energy from this reaction. In a medium containing 1 g yeast extract l-1, the addition of 10 mM benzaldehyde resulted in a twofold higher number of strain BR-10T cells. The mechanisms of benzaldehyde conversion by strains BOR-YT and BR-10T have not been described. Therefore, it was expected that the two strains represented novel micro-organisms.
In this report, we describe the phenotypic and phylogenetic characteristics of the mesophilic bacterium which converts benzaldehyde to benzoate and benzylalcohol (strain BOR-YT) and of the moderately thermophilic bacterium able to reduce benzaldehyde to benzylalcohol (strain BR-10T). On the basis of their phenotypic and phylogenetic characteristics, it is proposed that these two bacteria be named Soehngenia saccharolytica and Clostridium amygdalinum, respectively.
| METHODS |
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Media and cultivation.
Different media were used for cultivation of the isolates and the culture collection strains. A bicarbonate-phosphate-buffered medium was used. Medium preparation and cultivation of the isolates has been described previously (Parshina et al., 2000
). Strain BOR-YT was grown at 30 °C and strain BR-10T was grown at 45 °C. The bacteria were cultivated routinely in 120 ml serum bottles containing 50 ml medium. The amount of inoculum used was 12 %. For G+C content and DNADNA hybridization analyses, strain BOR-YT was grown with 2 g yeast extract l-1 plus 10 mM glucose and strain BR-10T was grown with 2 g yeast extract l-1 plus 10 mM crotonate. For the cultivation of Tissierella creatinini DSM 9508T, Clostridium Reinforced Medium (CRM), pH 8·3, supplemented with 0·5 M creatinine was used at 30 °C. CRM supplemented with 20 mmol serine l-1, 20 mmol threonine l-1 and 5 g yeast extract l-1 was used for cultivation of C. ultunense BST at 37 °C.
Microscopy.
Cell morphology of the isolates was investigated with a phase-contrast light microscope. Fine structure was studied using a JEM-100 electron microscope as described previously (Svetlichniy et al., 1991
). Gram staining was done according to standard procedures (Doetsch, 1981
).
Analytical methods.
Aromatic compounds (benzaldehyde, benzoate and benzylalcohol) and volatile fatty acids were analysed as described previously (Parshina et al., 2000
). Organic acids were analysed by HPLC (Merck) with an RI-detector. A Polyspher OAHY column (300 by 6·5 mm) was used. Hydrogen and carbon dioxide were analysed by using a Chrompack gas chromatograph (CP9001) equipped with a TCD-detector. The stainless steel column was filled with Molsieve 13X (6080 mesh). The TCD-detector run was at 100 °C; argon was used as the carrier gas. Sulfide was analysed by the method Trüper & Schlegel (1964)
.
Determination of temperature and pH optima.
For the determination of temperature optima, strain BOR-YT was cultivated in a medium containing 2 g yeast extract l-1 plus 2 g glucose l-1, and strain BR-10T was cultivated in a medium containing 2 g yeast extract l-1 plus 10 mmol crotonate l-1. Strain BOR-YT was incubated at 552 °C and strain BR-10T was incubated at 1070 °C. pH optima were determined by incubating strains BOR-YT and BR-10T at 30 and 45 °C, respectively, at initial pH values ranging from pH 5·0 to 9·0. The pH was adjusted by adding 6 M HCl or 6 M NaOH.
Physiological tests.
The following substrates were tested as carbon and energy sources (20 mmol l-1 each, unless indicated): yeast extract (2 g l-1), formate, acetate, propionate, isobutyrate, glucose, fructose, sucrose, xylose, arabinose, rhamnose, mannose, ribose, maltose, cellobiose, galactose, melibiose, lactose, cellulose, xylan, mannitol, casitone, inositol, methanol, ethanol, ethylene glycol, ethylamine, lactate, succinate, fumarate, crotonate, pyruvate, malate, starch (2 g l-1), glycerol, cysteine, serine, arginine, leucine, glycine, alanine, glutamate, methionine, casein (2 g l-1), casein hydrolysate (2 g l-1), peptone (2 g l-1), gelatin, betaine, H2/CO2 [80 % : 20 % (v/v) in the gas phase], creatine and creatinine. To investigate the utilization of electron acceptors, strains were cultivated in a medium containing 2 g yeast extract l-1. The following electron acceptors were tested: Na2SO4 (10 mM), Na2SO3 (2 mM), Na2S2O3 (10 mM), Na2S2O4 (10 mM), Na2S2O5 (10 mM), S0 (2 g l-1) and NaNO3 (2 g l-1). To test the ability of molecular nitrogen fixation, the medium described by Skinner (1971)
was used. Standard medium supplemented with 2 g yeast extract l-1 plus 10 mM pyruvate flushed with N2 served as a control. The aerotolerance of the strains was determined as described for Clostridium aerotolerans (van Gylswyk & van der Toorn, 1987
) in the medium supplied with 20 mM glucose. The air was injected into the closed bottles through a membrane filter. The volume of the air was 0·5100 % (v/v).
Biochemical tests.
Several physiological and biochemical characteristics of the cultures were analysed using API 20 E biochemical kits (Identification system for Enterobacteriaceae and other Gram-negative rods; bioMérieux). To test for the presence of catalase, cell material was exposed to 10 % H2O2.
Isolation of genomic DNA.
Wet biomass was washed with a solution containing 0·15 M NaCl and 0·1 M EDTA, pH 8·0, and transferred to a medium containing 0·6 M sucrose, 0·015 M Tris/HCl, pH 7·5, 0·015 M NaCl and 0·01 M EDTA. The bacterial cell wall was digested by the addition of 50 mg egg white lysozyme ml-1 (Fluka) to the suspension and incubation at 37 °C for 1 h and subsequent addition of 1 % SDS. Further purification was carried out according to previously described methods (Marmur, 1961
; Marmur & Doty, 1961
).
DNA G+C content determination.
This was done by thermal denaturation using a Pye Unicum SP 1800 spectrophotometer. The G+C content (mol%) was calculated as described by Owen et al. (1969)
.
DNADNA hybridization.
DNA homology was determined using the reassociation method described by De Ley et al. (1970)
.
16S rRNA gene sequence analysis.
This was done at the DSMZ. Approximately 95 % of the 16S rRNA gene sequence of the strains was determined by direct sequencing of PCR-amplified 16S rDNA. Genomic DNA extraction, PCR-mediated amplification of the 16S rDNA and purification of the PCR products was carried out as described by Rainey et al. (1996)
. Purified PCR products were sequenced using the ABI PRISM Dye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems) as described in the manufacturer's protocol. Sequence reactions were determined with an Applied Biosystems 373A DNA Sequencer.
The resulting sequence data from the isolates were put into the alignment editor AE2 (Maidak et al., 1996
), aligned manually and compared with representative 16S rRNA gene sequences of organisms belonging to the clostridia. For comparison, 16S rRNA gene sequences were obtained from the EMBL database or RDP (Maidak et al., 1996
). The 16S rRNA gene sequence similarity values were calculated by pairwise comparison of the sequences within the alignment. For construction of the phylogenetic dendrogram, the PHYLIP package (Felsenstein, 1993
) was used: pairwise evolutionary distances were computed from percentage similarities by the correction method of Jukes & Cantor (1969)
. Based on the evolutionary distance values, phylogenetic trees for strains BOR-YT and BR-10T (Figs 1 and 2![]()
, respectively) were constructed by the neighbor-joining method (Saitou & Nei, 1987
).
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| RESULTS AND DISCUSSION |
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Morphological characterization of strains BOR-YT and BR-10T
Strain BOR-YT.
Some morphological characteristics of strain BOR-YT can be found in the genus and species descriptions for Soehngenia and Soehngenia saccharolytica, respectively (see below). Strain BOR-YT was rod-shaped; its cells were slightly thickened in the middle and occurred singly, in pairs or in chains [Fig. Ia, supplementary data (http://ijs.sgmjournals.org)]. In the early-exponential phase of growth, cells were slightly motile by means of peritrichous flagella, but older cells lost their motility (Fig. Ib, supplementary data). Electron micrographs of thin sections revealed a cell-wall architecture typical for Gram-positive bacteria (Fig. Ic, supplementary data). Spores were formed in the medium supplemented with pyruvate and occasionally in the nitrogen-free medium. Colonies of strain BOR-YT on agar were rhizoid, resembled a snow-flake, were dark cream in colour and reached 1·01·2 mm in diameter.
Strain BR-10T.
Some morphological characteristics of strain BR-10T can be found in the species description for Clostridium amygdalinum (see below). The strain was Gram-positive (Fig. II, supplementary data), and motile in the early-exponential phase of growth. Cell chains, as well as swelling cells, were sometimes formed in the late-stationary phase of growth. Round, free spores were observed only in the nitrogen-free medium. Colonies of strain BR-10T on agar were circular, about 1 mm in diameter, creamy with a yellowish elevated centre and had a slightly undulating margin.
Physiological characterization and metabolism of strains BOR-YT and BR-10T
Strain BOR-YT.
Strain BOR-YT grew at initial pH values of between pH 6·5 and 7·5; the optimum pH for growth was around 7·0. The temperature range for growth was 1540 °C; the optimum temperature for growth was 3037 °C. Strain BOR-YT was anaerobic. A remarkable property of the strain was its aerotolerance. Strain BOR-YT grew until 50 % air in the gas phase at standing conditions in the medium supplemented with 20 mM glucose without reductant; however, it did not grow in non-reduced medium under air. The strain was capable of molecular nitrogen fixation. After 2 weeks cultivation, good growth was observed in a medium without NH4Cl, flushed with N2, supplemented with 10 mM of pyruvate and 8 mg yeast extract l-1. The strain was able to convert benzaldehyde. In our previous study (Parshina et al., 2000
), the conversion of benzaldehyde by strain BOR-YT was described in more detail. Strain BOR-YT required yeast extract in the medium (0·2 g l-1), and higher concentrations (12 g l-1) stimulated growth. In the medium supplemented with carbohydrates, fast cell lysis was observed at the stationary phase of growth. Strain BOR-YT used a wide range of carbon and energy sources, but could not utilize formate, acetate, propionate, isobutyrate, butyrate, casitone, inositol, glycerol, methanol, ethanol, p-cresol, casein, peptone, gelatin, lactate, succinate, fumarate, H2/CO2, creatine, creatinine, ethylene glycol, betaine, ethylamine, crotonate, arginine, leucine, glycine, alanine, glutamate, methionine or casein hydrolysate. The main products formed from the conversion of yeast extract were acetate, H2 and CO2. Products formed after fermentation of glucose were formate, H2, CO2, acetate and ethanol. Using the API 20 E system, strain BOR-YT showed
-galactosidase activity but no activity for arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase, urease, tryptophan desaminase, gelatinase or cytochrome oxidase. It also had positive reactions for H2S formation, indole and acetoin production, sorbitol and amygdalin fermentation and a negative reaction for citrate utilization.
Strain BR-10T.
Strain BR-10T grew between pH 6·5 and 8·0; the optimum pH for growth was 7·07·5. The temperature range for growth was 2060 °C; the optimum temperature for growth was 45 °C. The strain was aerotolerant. Growth occurred till 50 % of air in the gas phase at standing conditions. The strain did not fix molecular nitrogen. Strain BR-10T required yeast extract (12 g l-1) in the medium. Benzaldehyde, sulfite and thiosulfate were used as electron acceptors. Hydrogen in the gas phase instead of N2 served as an additional electron donor and this resulted in the stimulation of benzaldehyde conversion. Strain BR-10T used a wide range of carbon and energy sources, but could not utilize formate, acetate, propionate, isobutyrate, butyrate, methanol, benzoate, fumarate, malate, succinate, H2/CO2, galactose, rhamnose, lactose, mannose, cellulose, casein, casein hydrolysate, gelatin, aspartate, creatine, creatinine, ethylene glycol, ethylamine, arginine, leucine, lysine, alanine, glycine, glutamate or methionine. The main products formed from the conversion of yeast extract were H2, CO2 and acetate. Products from glucose fermentation were ethanol, acetate, H2 and CO2. Using the API 20 E system, strain BR-10Tshowed no
-galactosidase, arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase, urease, tryptophan desaminase, gelatinase or cytochrome oxidase activity. It had positive reactions for H2S, indole and acetoin production, and sorbitol and amygdalin fermentation, and a weak-positive reaction for citrate utilization.
Phylogenetic, G+C content and DNADNA hybridization analyses
Strain BOR-YT.
Comparative sequence analysis of the 16S rRNA gene sequence of strain BOR-YT showed that it is a member of cluster XII of the clostridia (Collins et al., 1994
) (Fig. 1
). This cluster is very heterogeneous. Among the bacteria most closely related to strain BOR-YT in the phylogenetic tree are members of the genus of spore-forming bacteria Clostridium and non-spore-forming Eubacterium and Tissierella. Strain BOR-YT showed highest sequence similarity with Tissierella creatinini DSM 9508T (93·6 %), Tissierella praeacuta NCTC 11158T (93·1 %), Tissierella creatinophila DSM 6911T (93·1 %), Clostridium hastiforme DSM 5675T (93·2 %) and C. ultunense DSM 10521T (92·2 %). Sequence similarity values of less than 97 % (Stackebrandt & Goebel, 1994
) justify the creation of a novel species for strain BOR-YT.
The G+C content of the DNA of strain BOR-YT was 43 mol%.
DNADNA hybridization of strain BOR-YT with C. ultunense BST and Tissierella creatinini DSM 9508T revealed reassociation values of 9 and 13 %, respectively. A DNA similarity value below 20 % is an indicator for a novel genus (Johnson, 1984
).
Strain BR-10T.
According to the results of a phylogenetic analysis, strain BR-10T falls into cluster XIVa of the clostridia (Collins et al., 1994
), with highest sequence similarity (9798 %) with a few representatives of the genus Clostridium (Fig. 2
). Strain BR-10T also showed 98 % sequence similarity with the sulfate-reducing bacterium Desulfotomaculum guttoideum (Gogotova & Vainstein, 1983
), but it does not use sulfate and thus does not belong to the genus Desulfotomaculum. All other phylogenetic neighbours belong to the genus Clostridium.
The G+C content of the DNA of strain BR-10T was 32 mol%.
Comparison of strains BOR-YT and BR-10T with related strains
Strain BOR-YT.
Table 1
gives characteristics useful for distinguishing strain BOR-YT from related species.
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On the basis of its phylogenetic, genetic and physiological properties, we propose to create a novel genus, Soehngenia, and a novel species, Soehngenia saccharolytica, to accommodate strain BOR-YT.
Strain BR-10T.
Table 2
gives characteristics useful for distinguishing strain BR-10T from related species.
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On the basis of its phylogenetic, genetic and physiological properties, we believe that strain BR-10T is clearly different from related species and can be considered as a novel species of Clostridium, namely, Clostridium amygdalinum.
Description of Soehngenia gen. nov.
Soehngenia [Soehn.ge'ni.a. N.L. fem. n. Soehngenia named in honour of Nicolas L. Soehngen, the founder and first head (19111937) of the Laboratory of Microbiology of Wageningen University, The Netherlands, where this strain was isolated and described].
Gram-positive. In the early-exponential phase of growth, cells are slightly motile by means of peritrichous flagella; older cells lose their motility. Rare terminal or subterminal spore formation. Mesophilic. Anaerobic, but aerotolerant. Fixes molecular nitrogen. Saccharolytic and weakly proteolytic. Major end products from yeast extract conversion are H2, CO2 and acetate. Products of glucose fermentation are formate, H2, CO2, acetate and ethanol.
Type species is Soehngenia saccharolytica.
Description of Soehngenia saccharolytica gen. nov., sp. nov.
Soehngenia saccharolytica (sac.cha.ro.ly'ti.ca. Gr. n. sakkharos sugar; Gr. adj. lytikos loosening, dissolving; N.L. fem. adj. saccharolytica sugar dissolving).
Has the features of the genus. Straight or slightly thickened at the middle rod-shaped cells (0·50·7 µm by 211 µm) that occur singly, in pairs or in chains. Cell chains are formed in the stationary phase of growth. Terminal or subterminal spores are formed occasionally on pyruvate medium or in nitrogen-free medium. Spores are round to oval in shape. Colonies on agar are rhizoid, resemble a snow-flake, are dark cream in colour and reach 1·01·2 mm in diameter. Fermentative metabolism. Able to grow till 50 % of air in the gas phase. Sulfite and thiosulfate are weakly used as electron acceptors (reduced to H2S). Sulfate, dithionite, disulfite, sulfur and nitrate are not used as electron receptors. Benzaldehyde is dismutated to benzoate and benzylalcohol. Catalase-negative. Produces indole. Does not liquefy gelatin. Substrates used as carbon and energy sources include yeast extract, glucose, fructose, sucrose, xylose, arabinose, rhamnose, mannose, ribose, maltose, cellobiose, galactose, melibiose, lactose, cellulose, xylan, mannitol, pyruvate, malate, starch, cysteine and serine. Minor product from yeast extract is NH+4. Moderate growth occurs in mineral medium supplemented with 0·2 g yeast extract l-1. Abundant growth occurs in mineral medium with 2 g yeast extract l-1or plus 10 mol glucose l-1 or some other carbohydrates. In medium supplemented with carbohydrates, cells lyse rapidly in the stationary phase of growth. Growth temperature range is 1540 °C; optimum growth at 3037 °C. pH range for growth is pH 6·07·5; optimum growth around pH 7·0.
The type strain is BOR-YT (=DSM 12858T=ATCC BAA-502T). Isolated from an anaerobic-digester sludge. G+C content of its DNA is 43 mol%.
Description of Clostridium amygdalinum sp. nov.
Clostridium amygdalinum (a.myg.da.li'num. L. neut. adj. amygdalinum made from almonds, referring to the smell of benzaldehyde, which is reduced by the type strain).
Oval or straight rod-shaped cells (0·51·0 µm by 0·510 µm) that occur singly, in pairs or in chains. In the early-exponential phase of growth, cells are motile by means of one terminal flagellum; older cells lose their motility. Cell chains, as well as swelling cells, are formed in the late-stationary phase of growth. Round, free spores are formed only in nitrogen-free medium. Colonies on agar are circular, about 1 mm in diameter, cream in colour with a yellowish elevated centre and have a slightly undulated margin. Gram-positive. Anaerobic, but aerotolerant. Growth occurs till 50 % of air in the gas phase. Does not fix molecular nitrogen. Obligate requirement for yeast extract (12 g l-1) in the growth medium. Substrates used as carbon and energy sources include yeast extract, glucose, sucrose, fructose, ribose, arabinose, xylose, melibiose, maltose, cellobiose, crotonate, casitone, pyruvate, lactate, ethanol, inositol, glycerol, mannitol, xylan, betaine, starch, casein, cysteine, serine and threonine. Catalase-negative. Produces indole. Does not liquefy gelatin. Major products formed from yeast extract are H2, CO2 and acetate; minor amounts of propionate, butyrate and valerate are formed. Products from glucose fermentation are ethanol, acetate, H2 and CO2. Benzaldehyde, sulfite and thiosulfite are used as electron acceptors. Sulfate, dithionite, disulfite, sulfur and nitrate are not used as electron acceptors. Moderately thermophilic. Temperature range for growth is 2060 °C; optimum growth at 45 °C. pH range for growth is pH 6·58·0; optimum growth at pH 7·07·5.
The type strain is BR-10T (=DSM 12857T=ATCC BAA-501T). Isolated from an anaerobic-digester sludge. G+C content of its DNA is 32 mol%.
| ACKNOWLEDGEMENTS |
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