| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Microbiological and Analytical Group, Food Research Laboratories, Mitsui Norin Co. Ltd, 223-1, Miyahara, Fujieda, Shizuoka 426-0133, Japan
2 Marine Biotechnology Institute Co. Ltd, 3-75-1, Heita, Kamaishi, Iwate 026-0001, Japan
3 Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1, Yayoi 1-chome, Bunkyo-ku, Tokyo 113-0032, Japan
Correspondence
Keiichi Goto
kgoto{at}mitsui-norin.co.jp
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
-Alicyclic fatty acids were the predominant lipid component of strains 4-A336T, 5-A83JT, 5-A167N, RB718T and S-TABT. No -alicyclic fatty acids were detected in strains 3-A191T, 5-A239-2O-AT or E-8, but iso- and anteiso-branched fatty acids and small amounts of straight-chain saturated fatty acids were detected instead. According to the DNA–DNA hybridization data and distinct morphological, physiological, chemotaxonomical and genetic traits, the eight strains represent six novel species within the genus Alicyclobacillus, for which the following names are proposed: Alicyclobacillus contaminans sp. nov. (type strain 3-A191T=DSM 17975T=IAM 15224T), Alicyclobacillus fastidiosus sp. nov. (type strain S-TABT=DSM 17978T=IAM 15229T), Alicyclobacillus kakegawensis sp. nov. (type strain 5-A83JT=DSM 17979T=IAM 15227T), Alicyclobacillus macrosporangiidus sp. nov. (type strain 5-A239-2O-AT=DSM 17980T=IAM 15370T), Alicyclobacillus sacchari sp. nov. (type strain RB718T=DSM 17974T=IAM 15230T) and Alicyclobacillus shizuokensis sp. nov. (type strain 4-A336T=DSM 17981T=IAM 15226T).
A table detailing the DNA base compositions and DNA–DNA hybridization values between the novel isolates and type strains of related Alicyclobacillus species is available as supplementary material with the online version of this paper.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
; Deinhard et al., 1987a, b; Wisotzkey et al., 1992; Dufresne et al., 1996; Albuquerque et al., 2000; Goto et al., 2002a, 2003; Matsubara et al., 2002; Tsuruoka et al., 2003; Simbahan et al., 2004; Karavaiko et al., 2005), two subspecies (Nicolaus et al., 1998) and two genomic species (Albuquerque et al., 2000; Goto et al., 2002b). The type species is Alicyclobacillus acidocaldarius (Darland & Brock, 1971; Wisotzkey et al., 1992). The genus is characterized by moderately thermophilic, acidophilic, strictly aerobic, endospore-forming bacilli with -alicyclic fatty acids (-cyclohexane or -cycloheptane) as the major membrane lipid component. Exceptions are Alicyclobacillus disulfidooxidans, which grows under mesophilic conditions, and Alicyclobacillus pomorum, which does not contain any -alicyclic fatty acids. The bacteria mainly inhabit hot springs and soil, but can also infest fruit and crops (Uchino & Doi, 1967; Darland & Brock, 1971; Hippchen et al., 1981; Deinhard et al., 1987a, b; Hiraishi et al., 1997; Nicolaus et al., 1998; Albuquerque et al., 2000; Goto et al., 2002b). Some species, in particular Alicyclobacillus acidoterrestris, can cause deterioration of beverages by the production of guaiacol, which has a creosote-like odour (Cerny et al., 1984; Sprittstoesser et al., 1994; Borlinghaus & Engel, 1997; Wisse & Parish, 1998; Eiroa et al., 1999; Duong & Jensen, 2000; Jensen, 2000). Accordingly, detection of contaminating Alicyclobacillus is an important quality control measure for the beverage industry.
We isolated 146 moderately thermophilic, acidophilic, spore-forming bacteria during the course of a microbiological survey of various beverages (including their raw materials) and environments. According to sequence analysis results for the hypervariable region of the 16S rRNA gene (Goto et al., 2002c; Kato et al., 2005), all of the strains belonged to the Alicyclobacillus clade but eight of the 146 strains were found to be distinct from recognized Alicyclobacillus species. The objective of the present study was to establish the taxonomic positions of the eight strains, by using a combination of polyphasic taxonomic approaches.
Type/reference strains of Alicyclobacillus species were obtained from the ATCC, DSMZ and IAM. Alicyclobacillus strains were grown on YSG agar [l–1: 2 g yeast extract, 1 g glucose, 2 g soluble starch and 15 g agar (pH 3.7 with 0.5 M H2SO4)] at the optimum growth temperature for each. Bacillus subtilis IAM 12118T was cultivated using the method recommended in the IAM strain catalogue.
Unless otherwise indicated, morphological observations and biochemical tests were performed using the methods of Darland & Brock (1971), Deinhard et al. (1987a, b), Albuquerque et al. (2000) and Goto et al. (2002c). Cultures were grown in either BAM liquid or BAM agar medium (Deinhard et al., 1987a, b). Cell growth was estimated by measuring turbidity at 578 nm. The pH range for growth was determined at 45 °C (for strain S-TABT), 50 °C (for strains 4-A336T, 5-A167N, 5-A239-2O-AT, E-8 and RB718T) and 55 °C (for strains 3-A191T and 5-A83JT) in BAM medium, with the pH adjusted using 1 M H2SO4. Acidification was examined with API 50 CH test strips (bioMérieux) in BAM basal salts medium (Albuquerque et al., 2000), at the optimum growth temperature. Guaiacol production was tested using a peroxidase kit (Kyokuto Pharmaceutical Industrial). All tests were conducted in triplicate.
Cellular fatty acids and menaquinones were analysed as described previously (Goto et al., 2002c, 2003). The DNA G+C content (mol%) was determined by using the method of Tamaoka & Komagata (1984) using HPLC with a YMC-Pack ODS-AQ AQ302 column (4.6x150 mm; YMC) and 10 mM H3PO4/10 mM KH2PO4 (pH 3.5) as the mobile phase.
Genomic DNA was extracted using a Qiagen Blood & Cell Culture DNA maxi kit (Qiagen) and purified by equilibrium centrifugation in CsCl/ethidium bromide gradients (Treismen, 1989) using an Optima MAX ultracentrifuge (80 000 r.p.m. x18 h; Beckman Coulter). Desalting was performed using an Ultrafree-4 centrifugal filter unit (Millipore).
Sequencing of the hypervariable region located at the 5'-end region of the 16S rRNA gene (about 270 bp) has been described previously (Goto et al., 2002c). Nearly complete 16S rRNA gene sequences were determined using a 16S rRNA gene kit (Applied Biosystems). Nucleotide sequences of gyrB were determined directly from PCR fragments using methods described by Yamamoto & Harayama (1995), Kasai et al. (2000) and Goto et al. (2003).
Sequence analysis was performed using Gene Works (version 2.0; IntelliGenetics) and the GenBank/EMBL/DDBJ databases. Multiple sequence alignments were performed using CLUSTAL W version 1.8 (Thompson et al., 1994). The gyrB nucleotide and deduced amino acid sequences were aligned using CLUSTAL W version 1.8, and then corrected manually. Alignment gaps and unidentified base positions were not taken into account for these calculations. Phylogenetic reconstructions were produced using MEGA3.1 (Kumar et al., 2004) with neighbour-joining (Saitou & Nei, 1987) based on the Kimura two-parameter model (Kimura, 1980) and maximum-parsimony (Lake, 1987). The robustness of individual branches was estimated by bootstrap analysis based on 1000 replicates (Felsenstein, 1985). The GenBank/EMBL/DDBJ accession numbers of 16S rRNA and gyrB gene sequences used for the phylogenetic analysis are shown in Figs 1 and 2, respectively.
|
|
using photobiotin-labelled DNA probes and microplates. Hybridization was carried out under stringent conditions (optimal renaturation temperature, +15 °C) for 3 h. Based on the DNA G+C contents of the type strains of Alicyclobacillus acidocaldarius subsp. acidocaldarius (61.9 mol%) and A. acidoterrestris (52.7 mol%), the renaturation temperatures were calculated to be 65 °C for strains 3-A191T, 4-A336T, 5-A83JT, 5-A167N, 5-A239-2O-AT and E-8, and 45 °C for strains RB718T and S-TABT. Each hybridization experiment was conducted at least three times. Strains E-8, RB718T and S-TABT were isolated from orange juice, liquid sugar and apple juice, respectively, using the standard dilution plating technique on YSG agar. Growth was at 45 °C. Strains RB718T and S-TABT were kindly provided by Ms Rie Yamamoto (Coca Cola Tokyo Research & Development Company Limited) and Ms Mikiko Yamanaka (Suntory Limited), respectively. Strains 3-A191T, 4-A336T, 5-A83JT, 5-A167N and 5-A239-2O-AT were isolated from soil samples collected from crop fields in four cities (Fuji, Fujieda, Kakegawa and Shizuoka) in the Shizuoka prefecture of Japan, using the standard dilution plating technique. Growth was at 50 °C.
Sequence analyses of the hypervariable region of the 16S rRNA gene (Goto et al., 2002c; Kato et al., 2005) showed that the eight strains (3-A191T, 4-A336T, 5-A83JT, 5-A167N, 5-A239-2O-AT, E-8, RB718T and S-TABT) belonged to the Alicyclobacillus clade. The strains were distinct from recognized Alicyclobacillus species in a hypervariable region-based tree (data not shown). Strains 3-A191T and 5-A83JT formed clusters with strains E-8 and 5-A167N, respectively, and had sequence similarities of 98.9 and 98.8 %, respectively. The remaining strains clustered with A. acidocaldarius and Alicyclobacillus genomic species 1 (Goto et al., 2006). All eight strains were further characterized using polyphasic taxonomic methods.
Basic differential phenotypic characteristics of the novel isolates and related Alicyclobacillus reference strains are shown in Table 1. Characteristics of strains 3-A191T and 5-A83JT were similar to those of strains E-8 and 5-A167N, respectively. All isolates were Gram-positive, but were Gram-variable after 5 days growth. Sporangia swelling was observed. After growth for 48 h on BAM agar, colonies were circular and were not pigmented. No growth occurred under anaerobic conditions. The strains grew well under acidic and moderately thermal conditions. Growth factors were not required, but growth was further increased by the addition of yeast extract to the inorganic medium. Oxidase and nitrate reductase activities were negative. Gas formation from glucose was not observed. Indole was not produced. Voges–Proskauer reaction was negative. Guaiacol was not produced. All strains grew on BAM agar containing 2 % (w/v) NaCl. Phenylalanine and tyrosine were not hydrolysed. Acid was produced from L-arabinose, ribose, D-xylose, D-galactose, D-glucose, D-fructose, D-mannose and trehalose, but not from ribitol, sorbitol, N-acetylglucosamine, L-arabitol, gluconate, 2-ketogluconate and 5-ketogluconate. All strains produced spores within several days of growth (BAM agar), with the exception of strain S-TABT, which produced only small amounts of spores after 10 days. In addition, many vegetative cells of strain S-TABT on YSG agar died within 7 days and therefore repeated subculturing was difficult using the most popular YSG medium for cultivation of Alicyclobacillus. The diameter of swollen sporangia from strain 5-A239-2O-AT was more than three times that of vegetative cells (Fig. 3).
|
|
).
Cellular fatty acid compositions are shown in Table 2. The predominant lipids were the fatty acids -cyclohexane, -cyclohexyl C17 : 0 and -cyclohexyl C19 : 0, for strains RB718T and S-TABT, whereas the most abundant fatty acids (75.0–91.3 %) for strains 4-A336T, 5-A83JT and 5-A167N were -cycloheptane, -cycloheptyl C18 : 0, -cycloheptyl C18 : 0 2-OH and -cycloheptyl C20 : 0.
|
The nearly complete nucleotide sequence of the 16S rRNA gene was determined for the eight isolates and for Alicyclobacillus tolerans DSM 16297T and Alicyclobacillus vulcanalis DSM 16176T. The sequences ranged in length from 1488 to 1526 bp, and 1468 bp were unambiguous for all isolates. The 16S rRNA gene sequence fragments were aligned with sequences available in the GenBank/EMBL/DDBJ databases and the phylogenetic positions of the strains were inferred by constructing a phylogenetic tree using either the neighbour-joining (Fig. 1
) or the maximum-parsimony (data not shown) methods. Phylogenetic analyses showed that all strains fell within the cluster composed of Alicyclobacillus species. In detail, strains 3-A191T and E-8 clustered with A. pomorum, strains 4-A336T, 5-A83JT and 5-A167N clustered with Alicyclobacillus herbarius, strain RB718T clustered with Alicyclobacillus hesperidum and strain S-TABT clustered with A. acidoterrestris with high bootstrap values. Strain 5-A239-2O-AT formed a deep lineage within the genus Alicyclobacillus (similarity values to the other species of 92.3–94.6 %). The sequence similarities among the isolates and the other type/reference strains of Alicyclobacillus species ranged from 90.2 to 99.7 %. Wisotzkey et al. (1992) proposed that 16S rRNA gene sequences must be at least 92 % similar to belong to the genus Alicyclobacillus, but several sequence matchings were below 92 % in this study. Similarity values between the isolates and either Bacillus tusciae NBRC 15312T, Sulfobacillus acidophilus DSM 10332T or Sulfobacillus thermosulfidooxidans DSM 9293T were all below 90 % (data not shown). The sequence similarity values between strains 3-A191T and E-8 and between strains 5-A83JT and 5-A167N were 99.8 and 99.3 %, respectively.
The nucleotide sequence of a fragment of the gyrB gene was determined for the eight isolates and for A. tolerans DSM 16297T and A. vulcanalis DSM 16176T. Of the fragments sequenced (sized 1167–1170 bp), 1142 bp were unambiguous and similar to positions 316–1485 in the Escherichia coli gyrB gene (Adachi et al., 1987). The gyrB sequence fragments were aligned with sequences available in the GenBank/EMBL/DDBJ databases and the phylogenetic relationships were determined as described for the 16S rRNA gene. The positions of strains in the gyrB-based tree were the same as in the 16S rRNA gene-based tree; however, relationships among the strains were more distinct in the gyrB tree (Figs 1 and 2). The position of strain 5-A239-2O-AT was still ambiguous, but the strain appeared to have some relationship to Alicyclobacillus cycloheptanicus and A. herbarius in the gyrB gene-based tree (Fig. 2). The gyrB gene sequences of the isolates exhibited 64.9–95.1 % similarity (mean 72.7 %) to the other type/reference strains of Alicyclobacillus species. By comparison, the sequence similarity values between strains 3-A191T and E-8 and between strains 5-A83JT and 5-A167N were 99.5 and 99.3 %, respectively.
DNA–DNA hybridization values between strains 5-A83JT and 5-A167N were 74 and 71 %, respectively, confirming that the two strains represent the same species (Wayne et al., 1987) (see Supplementary Table S1 available in IJSEM Online). Strains 3-A191T and E-8 were also assigned as representing a single species with values of 75 and 80 %, respectively. The DNA–DNA hybridization values of the isolates with type/reference strains of Alicyclobacillus species ranged from 0 to 37 %, which were well below the 70 % cut-off value recommended by Wayne et al. (1987) for the delineation of separate species.
In conclusion, based on the results of the polyphasic taxonomic analysis, the eight thermo-acidophilic, endospore-forming bacteria represent six novel species within the genus Alicyclobacillus. Here, we propose that the novel bacteria should be classified within the genus Alicyclobacillus, as Alicyclobacillus contaminans sp. nov. (strains 3-A191T and E-8), Alicyclobacillus fastidiosus sp. nov. (strain S-TABT), Alicyclobacillus kakegawensis sp. nov. (strains 5-A83JT and 5-A167N), Alicyclobacillus macrosporangiidus sp. nov. (strain 5-A239-2O-AT), Alicyclobacillus sacchari sp. nov. (strain RB718T) and Alicyclobacillus shizuokensis sp. nov. (strain 4-A336T).
Description of Alicyclobacillus contaminans sp. nov.
Alicyclobacillus contaminans (con.ta'mi.nans. L. part. adj. contaminans contaminating, referring to contamination of fruit juice).
Gram-positive but Gram-variable in old cultures, strictly aerobic, motile, endospore-forming straight rods with rounded ends (4.0–5.0 µm long and 0.8–0.9 µm wide). Endospores are ellipsoidal and subterminal with swollen sporangia. Colonies on BAM agar are non-pigmented (creamy white), circular, opaque, entire, umbonate and 3–5 mm in diameter after 48 h. Temperature range for growth is 35–60 °C; optimum growth temperature is 50–55 °C. The pH optimum is 4.0–4.5; growth does not occur at pH 3.0 or 6.0. Growth occurs in the presence of 0–2 % (w/v) NaCl but not 5 % (w/v) NaCl. Oxidase- and catalase-negative. Nitrate reduction, Voges–Proskauer test and indole production are negative. Gelatin and aesculin are hydrolysed, but phenylalanine, starch and tyrosine are not, and arbutin is variable. Acid is produced from glycerol, L-arabinose, ribose, D-xylose, D-galactose, D-glucose, D-fructose, D-mannose, mannitol, cellobiose, maltose, sucrose and trehalose. Variable from L-sorbose, rhamnose, salicin, lactose, 
-gentiobiose and D-tagatose. Major fatty acids are iso-C16 : 0 (13.7–16.9 %), iso-C17 : 0 (22.8–29.3 %) and anteiso-C17 : 0 (43.8–53.2 %). The main quinone is menaquinone 7. The DNA G+C content is 60.1–60.6 mol%.
The type strain, 3-A191T (=DSM 17975T=IAM 15224T), was isolated from soil of a crop field in Fuji city. Strain E-8 (=IAM 15228) was isolated from orange juice.
Description of Alicyclobacillus fastidiosus sp. nov.
Alicyclobacillus fastidiosus (fas.ti.di.o'sus. L. masc. adj. fastidiosus fastidious, referring to its fastidious character).
Gram-positive but Gram-variable in old cultures, strictly aerobic, non-motile, endospore-forming straight rods with rounded ends (4.0–5.0 µm long and 0.9–1.0 µm wide). Endospores are ellipsoidal and subterminal with swollen sporangia. Colonies on BAM agar are non-pigmented (creamy white), circular, opaque, entire, flat and 3–4 mm in diameter after 48 h. Temperature range for growth is 20–55 °C; optimum growth temperature is 40–45 °C. Optimum pH is 4.0–4.5; growth does not occur at pH 2.0 or 5.5. Growth occurs in the presence of 0–2 % (w/v) NaCl, but not at 5 % (w/v) NaCl. Oxidase-negative. Catalase-positive. Nitrate reduction, Voges–Proskauer test and indole production are negative. Gelatin is hydrolysed, but aesculin, arbutin, phenylalanine, starch and tyrosine are not. Acid is produced from D-arabinose, L-arabinose, ribose, D-xylose, methyl -xyloside, D-galactose, D-glucose, D-fructose, D-mannose, rhamnose, inositol, mannitol, melibiose, trehalose, D-raffinose, D-lyxose, D-tagatose, D-fucose and L-fucose. Major fatty acids are -cyclohexyl C17 : 0 and -cyclohexyl C19 : 0. The following fatty acids are present in smaller amounts: iso-C16 : 0 (8.3 %), iso-C17 : 0 (5.3 %) and anteiso-C17 : 0 (5.4 %). The main quinone is menaquinone 7. The DNA G+C content of the type strain is 53.9 mol%.
The type strain, S-TABT (=DSM 17978T=IAM 15229T), was isolated from apple juice.
Description of Alicyclobacillus kakegawensis sp. nov.
Alicyclobacillus kakegawensis (ka.ke.ga.wa.en'sis. N.L. masc. adj. kakegawensis pertaining to Kakegawa, a city in Shizuoka Prefecture, Japan, where the type strain was isolated).
Gram-positive but Gram-variable in old cultures, strictly aerobic, motile, endospore-forming straight rods with rounded ends (4.0–5.0 µm long and 0.6–0.7 µm wide). Endospores are oval and subterminal with swollen sporangia. Colonies on BAM agar are non-pigmented (creamy white), circular, opaque, entire, flat and 2–3 mm in diameter after 48 h. Temperature range for growth is 40–60 °C; optimum growth temperature is 50–55 °C. pH optimum is 4.0–4.5; growth does not occur at pH 3.0 or 6.5. Growth occurs in the presence of 0–2 % (w/v) NaCl but not at 5 % (w/v) NaCl. Oxidase-negative. Catalase weakly positive. Nitrate reduction, Voges–Proskauer test and indole production are negative. Aesculin and arbutin are hydrolysed, but gelatin, phenylalanine, starch and tyrosine are not. Acid is produced from D-arabinose, L-arabinose, ribose, D-xylose, L-xylose, D-galactose, D-glucose, D-fructose, D-mannose, L-sorbose, rhamnose, mannitol, sorbitol, methyl 
-D-mannoside, methyl -D-glucoside, amygdalin, salicin, cellobiose, maltose, lactose, sucrose, trehalose, xylitol, -gentiobiose, D-turanose, D-lyxose and D-arabitol. Variable acid production from erythritol, inositol, melezitose and D-tagatose. Major fatty acids are -cyclohexyl C18 : 0, -cyclohexyl C18 : 0 2-OH and -cyclohexyl C20 : 0. The following fatty acids are present in smaller amounts: C16 : 0 (4.2–8.8 %) and iso-C17 : 0 (0.5–4.7 %). The main quinone is menaquinone 7. The DNA G+C content is 61.3–61.7 mol%.
The type strain, 5-A83JT (=DSM 17979T=IAM 15227T), and strain 5-A167N (=IAM 15225) were isolated from soil of a crop field in Kakegawa city.
Description of Alicyclobacillus macrosporangiidus sp. nov.
Alicyclobacillus macrosporangiidus (ma.cro.spo.ran'gi.i.dus. Gr. adj. macros big; N.L. n. sporangium sporangia; L. suff. -idus suffix expressing a quality or tendency; N.L. masc. adj. macrosporangiidus having large sporangia).
Gram-positive but Gram-variable in old cultures, strictly aerobic, motile, endospore-forming straight rods with rounded ends (5.0–6.0 µm long and 0.7–0.8 µm wide). Endospores are oval and terminal with swollen sporangia. Colonies on BAM agar are non-pigmented (creamy white), circular, opaque, entire, convex and 2–4 mm in diameter after 48 h. Temperature range for growth is 35–60 °C; optimum growth temperature is 50–55 °C. pH optimum is 4.0–4.5; growth does not occur at pH 3.0 or 6.5. Growth occurs in the presence of 0–5 % (w/v) NaCl but not at 7 % (w/v) NaCl. Oxidase-negative. Catalase weakly positive. Nitrate reduction, Voges–Proskauer test and indole production are negative. Aesculin is hydrolysed, but gelatin, arbutin, phenylalanine, starch and tyrosine are not. Acid is produced from glycerol, D-arabinose, L-arabinose, ribose, D-xylose, L-xylose, D-galactose, D-glucose, D-fructose, D-mannose, L-sorbose, rhamnose, sorbitol, methyl -D-mannoside, salicin, maltose, lactose, sucrose, trehalose, xylitol, -gentiobiose, D-lyxose and D-arabitol. Major fatty acids are iso-C16 : 0 (44.2 %), iso-C17 : 0 (16.7 %) and anteiso-C17 : 0 (25.2 %). The main quinone is menaquinone 7. The DNA G+C content of the type strain is 62.5 mol%.
The type strain, 5-A239-2O-AT (=DSM 17980T=IAM 15370T), was isolated from soil of a crop field in Fujieda city.
Description of Alicyclobacillus sacchari sp. nov.
Alicyclobacillus sacchari (sac'cha.ri. N.L. gen. n. sacchari of sugar, referring to the source of isolation).
Gram-positive but Gram-variable in old cultures, strictly aerobic, motile, endospore-forming straight rods with rounded ends (4.0–5.0 µm long and 0.6–0.7 µm wide). Endospores are ellipsoidal and subterminal with swollen sporangia. Colonies on BAM agar are non-pigmented (creamy white), circular, opaque, entire, umbonate and 3–5 mm in diameter after 48 h. Temperature range for growth is 30–55 °C; optimum growth temperature is 45–50 °C. pH optimum is 4.0–4.5; growth does not occur at pH 2.0 or 6.0. Growth occurs in the presence of 0–2 % (w/v) NaCl, but not at 5 % (w/v) NaCl. Oxidase, catalase and nitrate reduction are negative. Voges–Proskauer test and indole production are negative. Arbutin, gelatin and starch are hydrolysed, but aesculin, phenylalanine and tyrosine are not. Acid is produced from glycerol, L-arabinose, ribose, D-xylose, methyl -xyloside, D-galactose, D-glucose, D-fructose, D-mannose, rhamnose, mannitol, methyl -D-glucoside, salicin, cellobiose, maltose, lactose, melibiose, sucrose, trehalose, inulin, melezitose, D-raffinose, glycogen, -gentiobiose and D-turanose. Major fatty acids are -cyclohexyl C17 : 0 and -cyclohexyl C19 : 0. The following fatty acids are present in smaller amounts: iso-C17 : 0 (2.4 %) and anteiso-C17 : 0 (4.6 %). The main quinone is menaquinone 7. The DNA G+C content of the type strain is 56.6 mol%.
The type strain, RB718T (=DSM 17974T=IAM 15230T), was isolated from liquid sugar.
Description of Alicyclobacillus shizuokensis sp. nov.
Alicyclobacillus shizuokensis (shi.zu.o.ken'sis. N.L. masc. adj. shizuokensis pertaining to Shizuoka, a city in Shizuoka Prefecture, Japan, where the type strain was isolated).
Gram-positive but Gram-variable in old cultures, strictly aerobic, motile, endospore-forming straight rods with rounded ends (4.0–5.0 µm long and 0.7–0.8 µm wide). Endospores are oval and subterminal with swollen sporangia. Colonies on BAM agar are non-pigmented (creamy white), circular, opaque, entire, convex and 1–2 mm in diameter after 48 h. Temperature range for growth is 35–60 °C; optimum growth temperature is 45–50 °C. pH optimum is 4.0–4.5; growth does not occur at pH 3.0 or 6.5. Growth occurs in the presence of 0–5 % (w/v) NaCl, but not 7 % (w/v) NaCl. Catalase-positive. Oxidase and nitrate reduction are negative. Voges–Proskauer test and indole production are negative. Aesculin and arbutin are hydrolysed, but gelatin, phenylalanine, starch and tyrosine are not. Acid is produced from L-arabinose, ribose, D-xylose, L-xylose, D-galactose, D-glucose, D-fructose, D-mannose, mannitol, salicin, cellobiose, maltose, melibiose, sucrose, trehalose and -gentiobiose. Major fatty acids are -cyclohexyl C18 : 0, -cyclohexyl C18 : 0 2-OH and -cyclohexyl C20 : 0. The following fatty acids are present in smaller amounts: C16 : 0 (6.1 %) and iso-C17 : 0 (4.0 %). The main quinone is menaquinone 7. The DNA G+C content of the type strain is 60.5 mol%.
The type strain, 4-A336T (=DSM 17981T=IAM 15226T), was isolated from soil of a crop field in Shizuoka city.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Albuquerque, L., Rainey, F. A., Chung, A. P., Sunna, A., Nobre, M. F., Grote, R., Antranikian, G. & De Costa, M. S. (2000). Alicyclobacillus hesperidum sp. nov. and a related genomic species from solfataric soils of São Miguel in the Azores. Int J Syst Evol Microbiol 50, 451–457.[Abstract]
Borlinghaus, A. & Engel, R. (1997). Alicyclobacillus incidence in commercial apple juice concentrate (AJC) supplies – method development and validation. Fruit Processing 7, 262–266.
Cerny, G., Hennlich, W. & Poralla, K. (1984). Fruchtsaftverderb durch Bacillen: isolierung und charakterisierung des verderbserregers. Z Lebens Unters Forsch 179, 224–227 (in German).[CrossRef]
Darland, G. & Brock, T. D. (1971). Bacillus acidocaldarius sp. nov., an acidophilic thermophilic spore-forming bacterium. J Gen Microbiol 67, 9–15.
Deinhard, G., Blanz, P., Poralla, K. & Altan, E. (1987a). Bacillus acidoterrestris sp. nov., a new thermotolerant acidophile isolated from different soils. Syst Appl Microbiol 10, 47–53.
Deinhard, G., Saar, J., Krischke, W. & Poralla, K. (1987b). Bacillus cycloheptanicus sp. nov., a new thermoacidophile containing -cycloheptane fatty acids. Syst Appl Microbiol 10, 68–73.
Dufresne, S., Bousquet, J., Boissinot, M. & Guay, R. (1996). Sulfobacillus disulfidooxidans sp. nov., a new acidophilic, disulfide-oxidizing, Gram-positive, spore-forming bacterium. Int J Syst Bacteriol 46, 1056–1064.
Duong, H.-A. & Jensen, N. (2000). Spoilage of iced tea by Alicyclobacillus. Food Australia 52, 292.
Eiroa, M. N. U., Junqueira, V. C. A. & Schmidt, F. (1999). Alicyclobacillus in orange juice: occurrence and heat resistance of spores. J Food Protection 62, 883–886.
Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
Goto, K., Matsubara, H., Mochida, K., Matsumura, T., Hara, Y., Niwa, M. & Yamasato, K. (2002a). Alicyclobacillus herbarius sp. nov., a novel bacterium containing -cycloheptane fatty acids, isolated from herbal tea. Int J Syst Evol Microbiol 52, 109–113.[Abstract]
Goto, K., Tanimoto, Y., Tamura, T., Mochida, K., Arai, D., Asahara, M., Suzuki, M., Tanaka, H. & Inagaki, K. (2002b). Identification of thermoacidophilic bacteria and a new Alicyclobacillus genomic species isolated from acidic environments in Japan. Extremophiles 6, 333–340.[CrossRef][Medline]
Goto, K., Mochida, K., Asahara, M., Suzuki, M. & Yokota, A. (2002c). Application of the hypervariable region of the 16S rDNA sequence as an index for the rapid identification of species in the genus Alicyclobacillus. J Gen Appl Microbiol 48, 243–250.[CrossRef][Medline]
Goto, K., Mochida, K., Asahara, M., Suzuki, M., Kasai, H. & Yokota, K. (2003). Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess -alicyclic fatty acids, and emended description of the genus Alicyclobacillus. Int J Syst Evol Microbiol 53, 1537–1544.
Goto, K., Mochida, K., Kato, Y., Asahara, M., Ozawa, C., Kasai, H. & Yokota, A. (2006). Diversity of Alicyclobacillus isolated from fruit juices and their raw materials, and emended description of Alicyclobacillus acidocaldarius. Microbiol Cult Coll 22, 1–14.
Hippchen, B., Roll, A. & Poralla, K. (1981). Occurrence in soil of thermo-acidophilic bacilli possessing -cyclohexane fatty acids and hopanoids. Arch Microbiol 129, 53–55.[CrossRef]
Hiraishi, A., Inagaki, K., Tanimoto, Y., Iwasaki, M., Kishimoto, N. & Tanaka, H. (1997). Phylogenetic characterization of a new thermoacidophilic bacterium isolated from hot spring in Japan. J Gen Appl Microbiol 43, 295–304.[Medline]
Jensen, N. (2000). Alicyclobacillus in Australia. Food Australia 52, 282–285.
Karavaiko, G. I., Bogdanova, T. I., Tourova, T. P., Kondrat'eva, T. F., Tsaplina, I. A., Egorova, M. A., Krasil'nikova, E. N. & Zakharchuk, L. M. (2005). Reclassification of ‘Sulfobacillus thermosulfidooxidans subsp. thermotolerans’ strain K1 as Alicyclobacillus tolerans sp. nov. and Sulfobacillus disulfidooxidans Dufresne et al. 1996 as Alicyclobacillus disulfidooxidans comb. nov., and emended description of the genus Alicyclobacillus. Int J Syst Evol Microbiol 55, 941–947.
Kasai, H., Tamura, T. & Harayama, S. (2000). Intrageneric relationship among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. Int J Syst Evol Microbiol 50, 127–134.[Abstract]
Kato, Y., Asahara, M., Arai, D., Goto, K. & Yokota, A. (2005). Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum. J Gen Appl Microbiol 51, 287–299.[CrossRef][Medline]
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequence. J Mol Evol 16, 111–120.[CrossRef][Medline]
Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.
Lake, J. A. (1987). A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol 4, 167–191.[Abstract]
Matsubara, H., Goto, K., Matsumura, T., Mochida, K., Iwaki, M., Niwa, M. & Yamasato, K. (2002). Alicyclobacillus acidiphilus sp. nov., a new thermo-acidophilic -alicyclic fatty acid-containing bacterium isolated from acidic beverages. Int J Syst Evol Microbiol 52, 1681–1685.[Abstract]
Nicolaus, B., Improta, R., Manca, C. M., Lama, L., Esposito, E. & Gambacorta, A. (1998). Alicyclobacilli from an unexplored geothermal soil in Antarctica: Mount Rittmann. Polar Biol 19, 133–141.[CrossRef]
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Simbahan, J., Drijber, R. & Blum, P. (2004). Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Spring, California, USA. Int J Syst Evol Microbiol 54, 1703–1707.
Sprittstoesser, D. F., Churey, J. J. & Lee, C. Y. (1994). Growth characteristics of aciduric sporeforming bacilli isolated from fruit juices. J Food Protection 57, 1080–1083.
Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef]
Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.
Treismen, R. (1989). Purification of plasmid DNA. In Molecular Cloning: a Laboratory Manual, 2nd edn, chapter 1, pp. 40–41. Edited by J. Sambrook, E. F. Fritsch & T. Maniatis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Tsuruoka, N., Isono, Y., Shida, O., Hemmi, H., Nakayama, T. & Nishio, T. (2003). Alicyclobacillus sendaiensis sp. nov., a novel acidophilic, slightly thermophilic species isolated from soil in Sendai, Japan. Int J Syst Evol Microbiol 53, 1081–1084.
Uchino, F. & Doi, S. (1967). Acido-thermophilic bacteria from thermal waters. Agr Biol Chem 31, 817–822.
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
Wisotzkey, J. D., Jurtshuk, J. R. P., Fox, G. E., Deinhard, G. & Poralla, K. (1992). Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov. Int J Syst Bacteriol 42, 263–269.
Wisse, C. A. & Parish, M. (1998). Isolation and enumeration of sporeforming, thermo-acidophilic, rod-shaped bacteria from citrus processing environments. Dairy Food Environ Sanitation 18, 504–509.
Yamamoto, S. & Harayama, S. (1995). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104–1109.[Abstract]
This article has been cited by other articles:
|
|
 |
|
  X. Guo, X.-Y. You, L.-J. Liu, J.-Y. Zhang, S.-J. Liu, and C.-Y. Jiang Alicyclobacillus aeris sp. nov., a novel ferrous- and sulfur-oxidizing bacterium isolated from a copper mine Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2415 - 2420. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-Y. Jiang, Y. Liu, Y.-Y. Liu, X.-Y. You, X. Guo, and S.-J. Liu Alicyclobacillus ferrooxydans sp. nov., a ferrous-oxidizing bacterium from solfataric soil Int J Syst Evol Microbiol, December 1, 2008; 58(12): 2898 - 2903. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Steven, M. Q. Chen, C. W. Greer, L. G. Whyte, and T. D. Niederberger Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost Int J Syst Evol Microbiol, June 1, 2008; 58(6): 1497 - 1501. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Imperio, C. Viti, and L. Marri Alicyclobacillus pohliae sp. nov., a thermophilic, endospore-forming bacterium isolated from geothermal soil of the north-west slope of Mount Melbourne (Antarctica) Int J Syst Evol Microbiol, January 1, 2008; 58(1): 221 - 225. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
