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1 Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
2 National University of Uzbekistan, Students Town, Tashkent, 700-174, Uzbekistan
Correspondence
Wan-Taek Im
wandra{at}kaist.ac.kr
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ABSTRACT |
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A neighbour-joining tree including representatives of a wider selection of Bacillus species is available as supplementary material in IJSEM Online.
These authors contributed equally to this work. 
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TOPABSTRACTMAIN TEXTREFERENCES |
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). The G+C contents (32–69 mol%) of the known Bacillus species, as well as the results of DNA–DNA hybridization experiments, have revealed the heterogeneity of the genus. The introduction of molecular methods, especially the use of 16S rRNA gene sequencing, has had a major impact on Bacillus taxonomy and has resulted in the splitting of the genus. In fact, in the last decade, 10 new genera have been separated from this original taxon (Wisotzkey et al., 1992; Ash et al., 1993; Shida et al., 1996; Heyndrickx et al., 1998; Wainø et al., 1999; Fortina et al., 2001; Nazina et al., 2001; Yoon et al., 2001). The genus currently includes more than 100 species (Euzéby, 2006). The members of this genus are considered to be ubiquitous because they have been isolated from a wide variety of aquatic and terrestrial environments, such as dust (Venkateswaran et al., 2003), river-mouth sediments (Ruiz-García et al., 2005), wastewater (Ajithkumar et al., 2002) and desert soils (Roberts et al., 1994). During the course of a study on the culturable aerobic/facultatively anaerobic bacterial community in soil from a ginseng field in Pocheon Province, South Korea, a large number of novel bacterial strains were isolated. In this study, we have characterized one of these isolates, namely strain Gsoil 1517T. Phenotypic, chemotaxonomic and phylogenetic analyses have established the affiliation of this isolate with the genus Bacillus. The data obtained also suggest that the isolate represents a novel species of the genus Bacillus.
Strain Gsoil 1517T was originally isolated from a soil sample from a ginseng field in Pocheon Province: the sample (1 g) was suspended in 10 ml 50 mM phosphate buffer (pH 7.0) and the suspension was spread on one-fifth-strength modified R2A agar plates [containing (l–1) 0.25 g tryptone, 0.25 g peptone, 0.25 g yeast extract, 0.125 g malt extract, 0.125 g beef extract, 0.25 g Casamino acids, 0.25 g soytone, 0.5 g glucose, 0.3 g soluble starch, 0.2 g xylan, 0.3 g sodium pyruvate, 0.3 g K2HPO4, 0.05 g MgSO4, 0.05 g CaCl2 and 15 g agar] after being serially diluted in 50 mM phosphate buffer (pH 7.0). The plates were incubated at 30 °C for 1 month. Single colonies on these plates were purified by transferring them onto new plates and subjecting them to an additional incubation on one-half-strength modified R2A for 3 days at 30 °C. The purified colonies were tentatively identified by partial sequencing of the 16S rRNA gene (Im et al., 2005). One isolate, Gsoil 1517T, was routinely cultured on R2A agar at 30 °C and maintained as a glycerol suspension (20 %, w/v) at –70 °C.
The Gram reaction was performed by using the non-staining method, as described by Buck (1982). The cell morphology was observed under a Nikon light microscope at x1000, with cells grown for 3 days at 30 °C on R2A agar. Catalase activity was determined by bubble production in 3 % (v/v) H2O2, and oxidase activity was determined using 1 % (w/v) tetramethyl-p-phenylenediamine. To study the assimilation of sole carbon sources, a defined liquid medium containing basal salt media (containing, l–1, 1.8 g K2HPO4, 1.08 g KH2PO4, 0.5 g NaNO3, 0.5 g NH4Cl, 0.1 g KCl, 0.1 g MgSO4 and 0.05 g CaCl2) was used. A vitamin solution (Widdel & Bak, 1992), a trace elements solution (SL-10; Widdel et al., 1983) and a selenite/tungstate solution (Tschech & Pfennig, 1984) were added to this medium, and the pH was then adjusted to 6.8. This liquid medium was poured into 96 wells and 25x stock solutions of carbon sources (filter-sterilized) were then added individually to each well. Growth was examined visually after incubation at 30 °C for 7 days. The negative-control well did not contain a carbon source. The positive-control culture was grown in a well containing R2A. Fermentative and oxidative carbohydrate metabolism were tested for by examining growth in O/F basal medium containing bromothymol blue (Atlas, 1993) and supplemented with 1 % carbohydrate [soft-agar stabs with (fermentative) and without (oxidative) a sterile mineral oil overlay]. The tubes containing O/F medium were incubated at 30 °C for 5 days. Some physiological characteristics were determined with API 20E galleries, according to the instructions of the manufacturer (bioMérieux). Anaerobic growth was examined in serum bottles by adding thioglycolate (1 g l–1) to R2A broth, in each case, to three serum bottles (25 ml) containing 23 ml R2A broth; the rubber caps were sealed with aluminium lids and then the upper air layer was replaced with nitrogen gas. An anaerobic nitrate reduction test (to determine the final electron acceptor) was performed in serum bottles by adding thioglycolate (1 g l–1) to R2A broth and substituting the air in the headspace with nitrogen gas while nitrate was added as KNO3 at concentrations of 10 mM. Aerobic nitrate reduction was later confirmed by inoculating, in each case, three serum bottles (25 ml) containing 12 ml R2A broth, while nitrate was added as KNO3 at a concentration of 10 mM. The reduction of nitrate was monitored by using an ion chromatograph (model 790 personal IC; Metrohm) equipped with a conductivity detector and an anion-exchange column (Metrosep Anion Supp 4; Metrohm). Tests for the degradation of DNA [DNASE agar (Scharlau), with DNase activity detected by flooding plates with 1 M HCl], casein, chitin, starch (Atlas, 1993), lipid (Kouker & Jaeger, 1987), xylan and cellulose (Ten et al., 2004) were performed and evaluated after 7 days. Growth at different temperatures (4, 15, 25, 30, 37, 42 and 45 °C) and various pH values (pH 4.0–10.0, using increments of 0.5 pH units) was assessed after 5 days incubation. Salt tolerance was tested on R2A agar supplemented with 1–10 % (w/v) NaCl after 5 days incubation. Growth at 30 °C on nutrient agar, trypticase soy agar (TSA; Difco) and MacConkey agar was also evaluated.
An almost-complete 16S rRNA gene sequence for strain Gsoil 1517T was determined as described below. Extraction of the genomic DNA was achieved using a commercial genomic DNA-extraction kit (Core Biosystem), and PCR-mediated amplification of the 16S rRNA gene and sequencing of the purified PCR product were carried out according to Kim et al. (2005). The full sequence of the 16S rRNA gene was compiled using SeqMan software (DNASTAR). The 16S rRNA gene sequences of related taxa were obtained from the GenBank database. Multiple alignments were performed by using the CLUSTAL_X program (Thompson et al., 1997). Gaps were edited in the BioEdit program (Hall, 1999). The evolutionary distances were calculated using the Kimura two-parameter model (Kimura, 1983). The phylogenetic tree was constructed using the neighbour-joining method (Saitou & Nei, 1987) and maximum parsimony (Fitch, 1971) in the MEGA3 program (Kumar et al., 2004), with bootstrap values based on 1000 replications (Felsenstein, 1985).
To measure the G+C content of the chromosomal DNA, the genomic DNA was extracted and purified as described by Moore (1995), enzymically degraded into nucleosides. The DNA G+C content was then determined as described by Mesbah et al. (1989), using reversed-phase HPLC. Isoprenoid quinones were extracted with chloroform/methanol (2 : 1, v/v), evaporated under vacuum conditions and re-extracted in n-hexane/water (1 : 1, v/v). The crude quinone in n-hexane was purified using silica Sep-Pak Vac cartridges (Waters) and subsequently analysed by HPLC, as described previously (Hiraishi et al., 1996). Cellular fatty acids were analysed in organisms grown on TSA for 2 days. The cellular fatty acids were saponified, methylated and extracted according to the protocol of the Sherlock Microbial Identification System (MIDI). The fatty acids were then analysed by gas chromatography (model 6890; Hewlett Packard) using the Microbial Identification software package (Sasser, 1990).
Strain Gsoil 1517T was Gram-positive, spore-forming, non-motile and rod-shaped. Central ellipsoidal endospores were observed in swollen sporangia. Colonies grown on R2A agar plates (Difco) for 2 days were smooth, shiny, circular, entire, light-yellowish white in colour and 1.5–2.0 mm in diameter. The oxidase and catalase reactions were positive. On R2A agar, the optimum temperature for growth was 30 °C and the optimum pH range was 6.5–7.0. Other physiological characteristics of strain Gsoil 1517T are summarized in the species description. The phenotypic and chemotaxonomic characteristics that differentiate strain Gsoil 1517T from related Bacillus species are listed in Table 1.
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). Strain Gsoil 1517T exhibited 16S rRNA gene sequence similarity of 96.8 % with respect to the type strain of B. funiculus and showed sequence similarities below 94.3 % with respect to the type strains of other Bacillus species with validly published names (see an extended tree, available as Supplementary Fig. S1 in IJSEM Online).
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).
The G+C content of the genomic DNA was 47.8 mol% and the predominant respiratory quinone was MK-7. The fatty acid profile of strain Gsoil 1517T is shown in Table 2 and was compared with those available for phylogenetically related Bacillus strains. Strain Gsoil 1517T contained large amounts of iso- and anteiso-branched fatty acids; the major components were 13-methyltetradecanoic acid (iso-C15 : 0), 12-methyltetradecanoic acid (anteiso-C15 : 0) and 12-methyltridecanoic acid (iso-C14 : 0), which is typical of members of the genus Bacillus (Kämpfer, 1994). Some qualitative and quantitative differences in fatty acid content could be observed between strain Gsoil 1517T and the phylogenetically closest relatives (Table 1
), perhaps because of differences in cultivation conditions (Kämpfer, 1994; Ajithkumar et al., 2002; Venkateswaran et al., 2003).
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), it is demonstrable that Gsoil 1517T is not affiliated with any known species of the genus Bacillus. Therefore, on the basis of the data presented above, strain Gsoil 1517T represents a novel species within the genus Bacillus, for which the name Bacillus panaciterrae sp. nov. is proposed.
Description of Bacillus panaciterrae sp. nov.
Bacillus panaciterrae (pa.na.ci.ter'rae. N.L. n. Panax -acis scientific name for ginseng; L. n. terra soil; N.L. gen. n. panaciterrae of soil of a ginseng field).
Cells are Gram-positive, rod-shaped, 0.5–0.8 µm in diameter and 3.0–5.0 µm in length, non-motile and occur singly or in chains. Central ellipsoidal endospores are observed in swollen sporangia. The optimum temperature for growth is 30 °C and the growth temperature range is between 20 and 45 °C. The minimum pH for growth lies between 5.0 and 5.5, the optimum pH is 6.5–7.0 and the maximum pH lies between 8.0 and 8.5. Tolerates 1 % (w/v) NaCl, but not 2 %. Growth occurs on TSA but not on MacConkey agar. Able to hydrolyse chitin, but not starch, cellulose, DNA, olive oil or xylan. The following substrates are utilized for growth: D-glucose, D-fructose, L-xylose, N-acetylglucosamine, pyruvate, acetate, 3-hydroxybutyrate, valerate, fumarate, salicin, citrate, lactate, malate, succinate, tartrate, sucrose, D-trehalose, gluconate, inositol (weakly), D-mannitol, xylitol, glycerol, inulin, L-alanine, L-arginine, L-asparagine, L-aspartate, L-glutamate, L-glutamine, L-histidine and L-proline. The following substrates are not utilized for growth: D-galactose, D-mannose, D-fucose, ethanol, L-rhamnose, L-sorbose, D- and L-arabinose, D-lyxose, D-ribose, D-xylose, formate, propionate, caprate, maleate, phenylacetate, benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate, malonate, glutarate, itaconate, adipate, suberate, oxalate, D-cellobiose, D-lactose, D-maltose, D-melibiose, D-raffinose, D-adonitol, dulcitol, D-sorbitol, amygdalin, methanol, glycogen, dextran, L-cysteine, glycine, L-isoleucine, L-leucine, L-lysine, L-threonine, L-methionine, L-phenylalanine, L-serine, L-tryptophan, L-tyrosine and L-valine. In API 20E tests, positive for gelatin hydrolysis and negative for 
-galactosidase, arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase, tryptophan deaminase, indole and H2S production, the Voges–Proskauer reaction and urease production. Acid is not produced from the following carbohydrates: L-arabinose, D-mannitol, inositol, D-sorbitol, L-rhamnose, sucrose, D-melibiose, D-glucose and amygdalin. The major fatty acids are iso-C15 : 0 (42.4 %), anteiso-C15 : 0 (17.4) and iso-C14 : 0 (9.7 %). The G+C content of genomic DNA is 47.8 mol%. MK-7 is the predominant respiratory quinone.
The type strain, Gsoil 1517T (=KCTC 13929T=CCUG 52470T=LMG 23408T), was isolated from soil from a ginseng field in Pocheon Province, South Korea.
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ACKNOWLEDGEMENTS |
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