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1 Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
2 Department of Biology, Texas Wesleyan University, Fort Worth, TX 76105, USA
3 National Research Institute of Fisheries, Food Processing Division, Yokohama, Kanagawa 236-8648, Japan
4 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
5 Division of Microbiology (HFT-250), National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079, USA
Correspondence
Mark E. Hart
mark.hart{at}fda.hhs.gov
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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A comparison of phenotypic characteristics of Bacillus tequilensis sp. nov. 10bT and other Bacillus species is available as supplementary material in IJSEM Online.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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). Comparison of approximately 95 % of the 16S rRNA gene sequences of 51 species of Bacillus revealed the genus to be also phylogenetically diverse (Ash et al., 1991b). The results of Ash et al. (1991b) caused the genus to be divided into five distinct groups, with the largest of these groups (RNA group 1, Bacillus sensu stricto) containing the type species, Bacillus subtilis, and 27 other species. Within RNA group 1, Bacillus atrophaeus, B. amyloliquefaciens, B. lautus, B. lentimorbus, B. licheniformis, B. popilliae, B. pumilus and B. subtilis form a distinct subgroup (Ash et al., 1991b). More recently, however, phylogenetic analysis and nucleotide motif determinations using the 16S rRNA gene sequence of B. lentimorbus ATCC 14707T and B. popilliae ATCC 14706T have resulted in the reclassification of these species in the genus Paenibacillus (Pettersson et al., 1999). In addition, B. lautus has also been reclassified in the genus Paenibacillus, based upon several genotypic and phenotypic analyses (Heyndrickx et al., 1996).
In addition to differences in DNA composition, certain members of the B. subtilis subgroup (Ash et al., 1991b), namely B. atrophaeus, B. amyloliquefaciens, B. licheniformis and B. subtilis, are difficult to differentiate phenotypically (Nakamura, 1987, 1989). For example, B. amyloliquefaciens can only be distinguished from B. subtilis by its ability to produce acid from inulin, the arrangement of its cells in chains and its centrally located spore (Logan & Berkeley, 1984). B. licheniformis can only be distinguished from B. subtilis by utilization of rhamnose, galactose and propionate, urease production, the arrangement of its cells in chains and its ability to grow anaerobically (Claus & Berkeley, 1986; Logan & Berkeley, 1984; Roberts et al., 1996), and pigmentation is the only phenotypic characteristic that can be used to differentiate B. subtilis from B. atrophaeus (Nakamura, 1989).
Because of the close phenotypic relatedness observed among these species and between other members of the genus Bacillus (Ash et al., 1991a; Harrell et al., 1995; Lechner et al., 1998), taxonomic revision of this genus has been suggested (Ash et al., 1991b; Logan & Berkeley, 1984; Rössler et al., 1991). In an effort to better characterize members of this genus, several studies have utilized molecular approaches as well as fatty acid analysis to characterize members of the B. subtilis subgroup (Cohan et al., 1991; Palmisano et al., 2001; Roberts & Cohan, 1995; Roberts et al., 1994, 1996) and strains within B. subtilis (Nakamura et al., 1999). For example, fatty acid composition, divergence in DNA sequence and levels of reassociation of genomic DNA were used to distinguish the newly described species Bacillus mojavensis and Bacillus vallismortis from B. subtilis (Roberts et al., 1994, 1996). Most recently, differences in phenotypic characteristics as well as cellular fatty acid composition, DNA–DNA hybridization and random amplified polymorphic DNA profiles have been used to differentiate three novel biosurfactant-producing species (Bacillus axarquiensis, Bacillus malacitensis and Bacillus velezensis) from other members of the B. subtilis subgroup (Ruiz-García et al., 2005a, b).
In the present study, a Gram-positive, spore-forming bacillus was isolated from a shaft-tomb sealed in approximately 74 AD at a site called Huitzilapa, near the city of Tequila in the Mexican state of Jalisco (Ramos de la Vega & López Mestas Camberos, 1996). Using conventional biochemical and whole-cell fatty acid analysis, sequence and phylogenetic comparisons of internal regions of the 16S rRNA and sodA genes, together with PFGE profiles of NotI-digested chromosomal DNA and DNA–DNA hybridization studies, the tomb isolate, strain 10bT, was shown to represent a distinct species that is highly related to members of the B. subtilis subgroup.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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. Bacillus strains were routinely grown overnight (15–18 h) at 37 °C in tryptic soy broth (TSB; Difco) with rotary aeration (180 r.p.m.) or on tryptic soy agar (TSA; TSB containing 1.5 % agar). Paenibacillus lentimorbus ATCC 14707T was grown at 27 °C in JB medium (per litre distilled water: tryptone, 5.0 g; yeast extract, 15.0 g; K2HPO4, 3.0 g; glucose, 2.0 g) or on TSA supplemented with 5 % defibrinated sheep blood (Remel), as recommended by the American Type Culture Collection (ATCC).
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) for 12 h at 37 °C. Spores were visualized by staining with malachite green and light microscopy. Strain 10bT together with B. amyloliquefaciens ATCC 23842, B. atrophaeus NRRL NRS-213T, B. licheniformis ATCC 12759, B. mojavensis NRRL B-14698T, B. subtilis 168 and B. vallismortis NRRL B-14890T were sent to the Texas Plant Disease Diagnostic Laboratory at Texas A&M University (College Station, TX, USA) for fatty acid methyl ester (FAME) analysis. The Bacillus strains were cultured on TSA for 15 h at 28 °C and the fatty acids were released from the cytoplasmic membrane by saponification. The free fatty acids were methylated and analysed by gas chromatography (Miller & Berger, 1985). Fatty acid profiles from three independent cultures grown on three separate days were averaged and used to determine species relatedness by comparison with the FAME database maintained at Texas A&M University.
In addition, bacterial growth at various pH values (4.0–8.0 in 0.5 unit increments) was measured by inoculating pH-adjusted 10 ml portions of TSB. Cultures were incubated at 37 °C for 24 h with rotary aeration (180 r.p.m.) and growth was monitored spectrophotometrically (OD550) at 3, 6, 9, 12 and 24 h. Growth at various temperatures (4, 25, 35, 45, 50 and 60 °C) was assessed on TSA plates. Haemolytic activity was assessed by streaking cultures onto TSA supplemented with 5 % defibrinated sheep blood. Strain 10bT was also characterized using API 20E and API 50 CH biochemical strips (bioMérieux), as recommended by Logan & Berkeley (1984). The strips were incubated at 37 °C for 48 h.
DNA isolation.
DNA used for PCR was isolated using the method of Daffonchio et al. (1998) and DNA for DNA–DNA hybridization studies was isolated using a modification of the method of Cutting & Vander Horn (1990).
PCR and sequencing of the 16S rRNA and sodA genes
16S rRNA gene.
Primers (5'-CGGGAGGCAGCAGTAGGGAAT-3' and 5'-CTCCCCAGGCGGAGTGCTTAAT-3') spanning nucleotides 343–889 of the 16S rRNA gene of Bacillus circulans (GenBank accession no. X60613; Cano & Borucki, 1995; Cano et al., 1994) were used to amplify a 546 bp fragment from DNA isolated from strain 10bT. The primer sequences used were taken from Cano et al. (1994). The amplified product from three independent PCRs was gel-purified, ligated into pCR2.1 (Invitrogen Life Technologies) and transformed into Escherichia coli INV
F' (Invitrogen), as recommended by the manufacturer. Plasmid DNA was isolated using a plasmid isolation kit (Bio-Rad), digested with EcoRI and resolved by agarose gel electrophoresis. Plasmids containing appropriately sized inserts were sequenced at the University of Arkansas for Medical Sciences DNA Sequencing Core Facility (Little Rock, AR, USA) using an automated DNA sequencer (Perkin-Elmer Biosystems). Sequences from each of the three independent PCRs were compared with each other to ensure that errors had not occurred.
sodA gene.
Degenerate primers (5'-CCITAYICITAYGAYGCIYTIGARCC-3' and 5'-ARRTARTAIGCRTGYTCCCAIACRTC-3') used to amplify an internal portion of the sodA gene from Streptococcus (Poyart et al., 1998), Enterococcus (Poyart et al., 2000) and Staphylococcus (Poyart et al., 2001) were used in combination with primers (5'-TCATGGCTTACGAACTTCCA-3' and 5'-CCACTTCGTCCCAGTTTACA-3') specific for the B. subtilis sodA gene (Kunst et al., 1997; GenBank/EMBL/DDBJ accession nos Z99104–Z99124) to amplify an internal portion of the sodA gene (sodAint) from each of the Bacillus strains used. The forward and reverse specific primers were used to amplify a 584 bp region from strain 10bT and B. mojavensis NRRL B-14698T. The degenerate forward and specific reverse primers were used to generate a 558 bp fragment from B. amyloliquefaciens ATCC 23842 and B. vallismortis NRRL B-14890T, and the specific forward and degenerate reverse primers were used to amplify a 516 bp region from B. atrophaeus NRRL NRS-213T and P. lentimorbus ATCC 14707T. The amplified product from three independent PCRs was gel-purified, cloned and sequenced, as described above.
Sequence analysis.
The 16S rRNA gene sequences generated in this study together with those of B. subtilis 168, B. atrophaeus JCM 9070T, B. licheniformis KL-164, B. mojavensis KL-198, B. vallismortis DSM 11031T and the outgroup Lactobacillus casei ATCC 393T were aligned and sequence similarity was assessed using DNAMan software (Lynnon BioSoft). Likewise, DNAMan software was used to align and determine the similarity of the sodAint sequences from the tomb isolate, B. amyloliquefaciens ATCC 23842, B. atrophaeus NRRL NRS-213T, P. lentimorbus ATCC 14707T, B. licheniformis ATCC 27811, B. mojavensis NRRL B-14698T, B. subtilis 168, B. vallismortis NRRL B-14890T and the outgroup Staphylococcus aureus RN6390. In addition, putative SodAint amino acid sequences from these strains were also aligned and similarity was assessed using DNAMan software.
Phylogenetic relationships between strain 10bT and other Gram-positive, spore-forming bacilli were inferred from phylogenetic comparison of the 16S rRNA and sodA nucleotide sequences and SodAint amino acid sequences using parsimony (DNAPARS) and maximum-likelihood algorithms (DNAML and DNAMLK) available in PHYLIP (Felsenstein, 1993). Gene sequences were aligned using DNAMan. Indels noted during sequence alignment were treated as unknowns in the phylogenetic analyses. Phylogenetic comparison performed using maximum-likelihood (DNAML algorithm) estimates branch length after first estimating the relative frequency of bases at all sites in the sequences to calculate rates of transition and transversion. Confidence limits on the resulting tree-branch lengths and the probability of non-zero lengths were calculated. Maximum-parsimony (DNAPARS) was also used to compare sequences, assuming that the shortest tree(s) might produce an accurate hypothesis of phylogenetic relationships. Maximum-likelihood and parsimony-derived trees were bootstrapped using 1000 random samples of the original taxon by character matrix sequences with replacement using the SEQUENCEBOOT procedure (Felsenstein, 1993). The input order of sequences was jumbled to ensure that all sequences would be considered first in tree construction. Each of the tree-producing algorithms was run using the 1000 resampled data matrix. All resulting trees were evaluated to estimate majority rule consensus trees using the CONSENSUS procedure to produce bootstrapped phenograms (Felsenstein, 1993). Trees were treated as unrooted, although the outgroup designation option was included to polarize character states.
PFGE.
Cells for PFGE were prepared as described by Smeltzer et al. (1992) and as instructed by the manufacturer (Bio-Rad). Chromosomal DNA was digested with NotI and portions of agarose plugs were placed in wells formed in 1.2 % agarose (Bio-Rad). Electrophoresis was carried out at 3 V cm–1 for 40 h, with a ramp time of 18 s (Itaya, 1997). DNA bands were visualized with ethidium bromide staining and ultraviolet light. Bands were compared with a lambda DNA marker (Bio-Rad) and sized using AlphaEase software (Alpha Innotech).
DNA–DNA hybridization.
The microplate method of Ezaki et al. (1989) together with the photobiotin-labelling and colorimetric detection systems of Satomi et al. (1997) were used to determine the percentage relatedness between strains.
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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). Qualitative differences between strain 10bT and the other Bacillus species examined were not observed. However, significant differences with respect to the amounts of several major and minor fatty acids were found (Table 3).
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). Comparison of the sequences revealed that the 16S rRNA gene sequence of strain 10bT was 99.8 % similar to that of B. licheniformis KL-164, 99.6 % similar to B. mojavensis KL-198 and 99.3 % similar to B. subtilis 168, B. vallismortis DSM 11031T and B. atrophaeus JCM 9070T. As a point of reference, the 16S rRNA gene sequence of B. subtilis 168 was 99.4 % similar to that of B. licheniformis KL-164.
In previous studies (Poyart et al., 1998, 2000, 2001), a highly conserved region of the sodA gene from Streptococcus, Enterococcus and coagulase-negative Staphylococcus species was amplified, sequenced and compared to determine whether this gene could be used to differentiate members of these genera. The discriminatory power of the sodAint amplified region was compared with that of the 16S rRNA gene and genes encoding heat shock protein 60 (hsp60) and was found to exhibit a greater divergence than either the 16S rRNA or hsp60 genes (Poyart et al., 1998, 2000, 2001). Because of the discriminatory power exhibited by the sodAint sequence for these Gram-positive cocci, a similar region was amplified from strain 10bT and other members of the B. subtilis subgroup. The sodAint nucleotide sequence of strain 10bT was found to be 94.9 % similar to that of sodAint in B. subtilis 168, whereas the sequence from B. mojavensis NRRL B-14698T was found to be 93.8 % similar to that of strain 10bT. B. atrophaeus NRRL NRS-213T was 86.2 % similar to strain 10bT and the sodAint sequences of B. amyloliquefaciens ATCC 23842 and B. vallismortis NRRL B-14890T were 83.8 % similar to that of strain 10bT. The same sequence from B. licheniformis ATCC 27811 was found to be only 79.8 % similar to that of strain 10bT and 82.4 % similar to the sodAint sequence of B. mojavensis NRRL B-14698T. The sodAint sequence of B. subtilis 168 was 95.2 % similar to that of B. mojavensis NRRL B-14698T.
The putative amino acid sequence of the sodAint sequence from strain 10bT was shown to be 97.8 % similar to that of B. subtilis 168, 96.3 % similar to that of B. mojavensis NRRL B-14698T and 91.2 % similar to that of B. atrophaeus NRRL NRS-213T. The same amino acid sequence was also 89.6 % similar to those of B. amyloliquefaciens ATCC 23842 and B. vallismortis NRRL B-14890T, and only 83.8 % similar to that of B. licheniformis ATCC 27811. The SodAint sequence of B. subtilis 168 was 98.5 % similar to that of B. mojavensis NRRL B-14698T.
Phylogeny of strain 10bT and other Bacillus species
The 16S rRNA gene sequence similarity between strain 10bT and its closest relatives, B. subtilis 168, B. mojavensis KL-198 and B. licheniformis KL-164, was close to 100 % (99.3–99.8 %). Phylogenetic sequence comparison using maximum-likelihood estimates of relatedness also indicated a close relationship between strain 10bT, B. mojavensis KL-198 and B. licheniformis KL-164, whereas strict parsimony includes these three taxa together with B. subtilis 168 and B. atrophaeus JCM 9070T. Nevertheless, bootstrap estimates, using strict parsimony (data not shown) and maximum-likelihood (Fig. 1a), indicated that 81 and 89 % of trees, respectively, resolved this group of species. Bootstrap estimates of the majority rule consensus trees obtained from maximum-likelihood estimates of sequence divergence based on the 16S rRNA gene sequences indicate that strain 10bT, B. mojavensis KL-198 and B. licheniformis KL-164 are indistinguishable, each pair of taxa sharing a terminal node one-third of the time. Furthermore, the bootstrap estimates indicate that strain 10bT, B. mojavensis KL-198, B. licheniformis KL-164, B. subtilis 168 and B. atrophaeus JCM 9070T comprise a monophyletic group, when compared with L. casei ATCC 393T and B. vallismortis DSM 11031T (Fig. 1a).
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) included strain 10bT and B. subtilis 168, whereas 96 % of the trees using strict parsimony also contained these two species (data not shown). Nevertheless, all maximum-likelihood estimates indicate that the branch lengths separating strain 10bT and B. subtilis 168 are of non-zero length. Both maximum-likelihood and strict parsimony include B. mojavensis NRRL B-14698T as a close relative to strain 10bT and B. subtilis 168. Furthermore, this analysis supports the suspected similarity of B. atrophaeus NRRL NRS-213T and strain 10bT while at the same time suggesting that B. licheniformis ATCC 27811 is related, but not as closely as suggested by the 16S rRNA gene analysis. Nevertheless, all maximum-likelihood estimates indicate that branch lengths separating Bacillus strain 10bT and B. subtilis 168 are of non-zero length (data not shown). The phylogenetic analysis of the sodA sequence corroborates the apparent speciation while noting the similarity between strain 10bT and B. atrophaeus NRRL NRS-213T, B. licheniformis ATCC 27811, B. mojavensis NRRL B-14698T and B. subtilis 168.
The 16S rRNA gene sequence comparison suggests that strain 10bT is closely related to four Bacillus species; namely, B. mojavensis KL-198, B. licheniformis KL-164, B. atrophaeus JCM 9070T and B. subtilis 168. On the other hand, phylogenetic comparison of the 455 bp sequence of sodAint confirmed that strain 10bT is related to B. subtilis 168. Bootstrap values for DNA sequence comparison indicate that 95 % of trees included strain 10bT and B. subtilis 168 at the same node (Fig. 1b). Maximum-likelihood methods indicate that the two taxa are similar but the branches from the conjoining node have non-zero lengths in both cases, suggesting they are distinct species. The SodAint amino acid sequence phylogeny reproduced the nucleic acid relationships by depicting strain 10bT and B. subtilis 168 as having a common ancestor and suggested that this group and B. mojavensis NRRL B-14698T share a common ancestor (Fig. 1c). Similar to the nucleic acid sequence, the maximum-likelihood amino acid phylogeny indicates that the branch separating strain 10bT from B. subtilis 168 has a non-zero length.
PFGE analysis of strain 10bT and various Bacillus strains
Chromosomal DNA isolated from strain 10bT, B. licheniformis ATCC 12759, B. atrophaeus NRRL NRS-213T, B. mojavensis NRRL B-14698T, B. vallismortis NRRL B-14890T, B. amyloliquefaciens ATCC 23842 and three strains of B. subtilis (168, BGSC 1E60 and BGSC 1A304) was digested with NotI and fragments were resolved by PFGE (Fig. 2a). Electrophoretic parameters used provided significant separation of fragments in the 48.5–242.5 kbp range. The resulting banding patterns indicate that strain 10bT is considerably different from the other Bacillus species examined. As a control, three strains of B. subtilis (168, BGSC 1E60 and BGSC 1A304) were used and, apart from a 243 kbp fragment missing from BGSC 1A304, the banding patterns for all three strains were identical. All remaining species exhibited unique banding patterns (Fig. 2a, b).
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. Reassociation values ranged from 22 % with B. licheniformis ATCC 12759 to 56 % with B. subtilis 168. Such high percentages are not uncommon between species of the genus Bacillus (La Duc et al., 2004). The DNA–DNA reassociation values for strain 10bT were approximately 55 % with four strains of B. subtilis (NRRL B-23049T, NRRL B-14472, 168 and IAM 1026) and its subspecies and approximately 46 and 49 % with B. mojavensis NRRL B-14698T and B. vallismortis NRRL B-14890T, respectively. Such close clustering was also observed in this study under the same experimental conditions when DNA from B. subtilis strains was hybridized with DNA from B. vallismortis NRRL B-14890T (45–50 %) and B. mojavensis NRRL B-14698T (40–48 %). These data strongly indicate that strain 10bT represents a novel species of the genus Bacillus according to the criteria for differentiation of bacterial species (Wayne et al., 1987).
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Description of Bacillus tequilensis sp. nov.
Bacillus tequilensis (te.qui.len'sis. N.L. masc. adj. tequilensis referring to Tequila, Mexico).
Vegetative cells are rod-shaped and 0.9x4.0 µm in size. Primarily occur as single cells, although a few chains of two to four cells are also seen. Gram-positive, motile and catalase- and oxidase-positive. Does not grow anaerobically. Grows at pH 5.5–8.0 and 25–50 °C. Spores are located centrally, without swollen sporangia. Colonies on TSA after 24 h at 37 °C are round, smooth, yellowish in colour and approximately 3.8±0.2 mm in diameter. Casein, starch and gelatin are hydrolysed. Nitrate is reduced to nitrogen gas and citrate is utilized. Tryptophan, ONPG, arginine, lysine and ornithine are decomposed, but not sodium thiosulfate or urea. Produces indole and acetylmethylcarbinol. Non-haemolytic on 5 % sheep blood agar. Acid is produced from glycerol, D-arabinose, L-arabinose, D-ribose, D-xylose, L-xylose, adonitol, galactose, D-glucose, D-fructose, D-mannose, L-sorbose, rhamnose, dulcitol, inositol, mannitol, sorbitol, methyl -D-glucoside, N-acetylglucosamine, amygdalin, arbutin, aesculin, salicin, cellobiose, maltose, lactose, melibiose, sucrose, trehalose, inulin, D-raffinose, starch, glycogen, xylitol, 
-gentiobiose, D-turanose, D-lyxose, D-tagatose, D-fucose, L-fucose, D-arabitol and L-arabitol. Acid is not produced from erythritol, methyl -D-xyloside, methyl -D-mannoside, melezitose, gluconate, 2-ketogluconate or 5-ketogluconate. Major whole-cell fatty acids are 15 : 0 anteiso (46.3 %), 15 : 0 iso (18.8 %), 17 : 0 anteiso (12.8 %), 17 : 0 iso (6.2 %), 16 : 0 (4.8 %) and 14 : 0 iso (1.3 %).
The type strain is strain 10bT (=ATCC BAA-819T=NCTC 13306T), which was isolated from an approximately 2000-year-old shaft-tomb at a site called Huitzilapa, near the city of Tequila in the Mexican state of Jalisco.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D. (1991b). Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13, 202–206.
Cano, R. J. & Borucki, M. K. (1995). Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber. Science 268, 1060–1064.
Cano, R. J., Borucki, M. K., Higby-Schweitzer, M., Poinar, H. N., Poinar, G. O., Jr & Pollard, K. J. (1994). Bacillus DNA in fossil bees: an ancient symbiosis? Appl Environ Microbiol 60, 2164–2167.
Claus, D. & Berkeley, R. C. W. (1986). Genus Bacillus Cohn 1872, 174AL. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1105–1139. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
Cohan, F. M., Roberts, M. S. & King, E. C. (1991). The potential for genetic exchange by transformation within a natural population of Bacillus subtilis. Evolution 45, 1393–1421.[CrossRef]
Cutting, S. M. & Vander Horn, P. B. (1990). Genetic analysis. In Molecular Biological Methods of Bacillus, pp. 27–74. Edited by C. R. Harwood & S. M. Cutting. Chichester: Wiley.
Daffonchio, D., Borin, S., Frova, G., Manachini, P. L. & Sorlini, C. (1998). PCR fingerprinting of whole genomes: the spacers between the 16S and 23S rRNA genes and of intergenic tRNA gene regions reveal a different intraspecific genomic variability of Bacillus cereus and Bacillus licheniformis. Int J Syst Bacteriol 48, 107–116.
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. (1993). PHYLIP (phylogeny inference package), version 3.5c. Department of Genome Sciences, University of Washington, Seattle, USA.
Harrell, L. J., Andersen, G. L. & Wilson, K. H. (1995). Genetic variability of Bacillus anthracis and related species. J Clin Microbiol 33, 1847–1850.[Abstract]
Heyndrickx, M., Vandemeulebroecke, K., Scheldeman, P., Kersters, K., De Vos, P., Logan, N. A., Aziz, A. M., Ali, N. & Berkeley, R. C. W. (1996). A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended descriptions of P. lautus and of P. peoriae. Int J Syst Bacteriol 46, 988–1003.
Itaya, M. (1997). Physical map of the Bacillus subtilis 166 genome: evidence for the inversion of an approximately 1900 kb continuous DNA segment, the translocation of an approximately 100 kb segment and the duplication of a 5 kb segment. Microbiology 143, 3723–3732.
Kunst, F., Ogasawara, N., Moszer, I. & 148 other authors (1997). The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390, 249–256.[CrossRef][Medline]
La Duc, M. T., Satomi, M., Agata, N. & Venkateswaran, K. (2004). gyrB as a phylogenetic discriminator for members of the Bacillus anthracis-cereus-thuringiensis group. J Microbiol Methods 56, 383–394.[CrossRef][Medline]
Lechner, S., Mayr, R., Francis, K. P., Prüß, B. M., Kaplan, T., Wießner-Gunkel, E., Stewart, G. S. A. B. & Scherer, S. (1998). Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. Int J Syst Bacteriol 48, 1373–1382.
Logan, N. A. & Berkeley, R. C. (1984). Identification of Bacillus strains using the API system. J Gen Microbiol 130, 1871–1882.
Miller, L. & Berger, T. (1985). Bacteria identification by gas chromatography of whole cell fatty acids, Gas Chromatography Application Note 228–41. Palo Alto, CA: Hewlett-Packard Co.
Nakamura, L. K. (1987). Deoxyribonucleic acid relatedness of lactose-positive Bacillus subtilis strains and Bacillus amyloliquefaciens. Int J Syst Bacteriol 37, 444–445.
Nakamura, L. K. (1989). Taxonomic relationship of black-pigmented Bacillus subtilis strains and a proposal for Bacillus atrophaeus sp. nov. Int J Syst Bacteriol 39, 295–300.
Nakamura, L. K., Roberts, M. S. & Cohan, F. M. (1999). Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int J Syst Bacteriol 49, 1211–1215.
Palmisano, M. M., Nakamura, L. K., Duncan, K. E., Istock, C. A. & Cohan, F. M. (2001). Bacillus sonorensis sp. nov., a close relative of Bacillus licheniformis, isolated from soil in the Sonoran Desert, Arizona. Int J Syst Evol Microbiol 51, 1671–1679.[Abstract]
Pettersson, B., Rippere, K. E., Yousten, A. A. & Priest, F. G. (1999). Transfer of Bacillus lentimorbus and Bacillus popilliae to the genus Paenibacillus with emended descriptions of Paenibacillus lentimorbus comb. nov. and Paenibacillus popilliae comb. nov. Int J Syst Bacteriol 49, 531–540.
Poyart, C., Quesne, G., Coulon, S., Berche, P. & Trieu-Cuot, P. (1998). Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J Clin Microbiol 36, 41–47.
Poyart, C., Quesnes, G. & Trieu-Cuot, P. (2000). Sequencing the gene encoding manganese-dependent superoxide dismutase for rapid species identification of enterococci. J Clin Microbiol 38, 415–418.
Poyart, C., Quesne, G., Boumaila, C. & Trieu-Cuot, P. (2001). Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target. J Clin Microbiol 39, 4296–4301.
Ramos de la Vega, J. & López Mestas Camberos, M. L. (1996). Datos preliminares sobre el descubrimiento de una tumba de tiro en el sitio de Huitzilapa, Jalisco. Ancient Mesoamerica 7, 121–134 (in Spanish).
Roberts, M. S. & Cohan, F. M. (1995). Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49, 1081–1094.[CrossRef]
Roberts, M. S., Nakamura, L. K. & Cohan, F. M. (1994). Bacillus mojavensis sp. nov., distinguishable from Bacillus subtilis by sexual isolation, divergence in DNA sequence, and differences in fatty acid composition. Int J Syst Bacteriol 44, 256–264.
Roberts, M. S., Nakamura, L. K. & Cohan, F. M. (1996). Bacillus vallismortis sp. nov., a close relative of Bacillus subtilis, isolated from soil in Death Valley, California. Int J Syst Bacteriol 46, 470–475.
Rössler, D., Ludwig, W., Schleifer, K. H., Lin, C., McGill, T. J., Wisotzkey, J. D., Jurtshuk, P., Jr & Fox, G. E. (1991). Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies. Syst Appl Microbiol 14, 266–269.[Medline]
Ruiz-García, C., Béjar, V., Martínez-Checa, F., Llamas, I. & Quesada, E. (2005a). Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain. Int J Syst Evol Microbiol 55, 191–195.
Ruiz-García, C., Quesada, E., Martínez-Checa, F., Llamas, I., Urdaci, M. C. & Béjar, V. (2005b). Bacillus axarquiensis sp. nov. and Bacillus malacitensis sp. nov., isolated from river-mouth sediments in southern Spain. Int J Syst Evol Microbiol 55, 1279–1285.
Satomi, M., Kimura, B., Mizoi, M., Sato, T. & Fujii, T. (1997). Tetragenococcus muriaticus sp. nov., a new moderately halophilic lactic acid bacterium isolated from fermented squid liver sauce. Int J Syst Bacteriol 47, 832–836.
Schaeffer, P., Millet, J. & Aubert, J.-P. (1965). Catabolic repression of bacterial sporulation. Proc Natl Acad Sci U S A 54, 704–711.
Smeltzer, M. S., Gill, S. R. & Iandolo, J. J. (1992). Localization of a chromosomal mutation affecting expression of extracellular lipase in Staphylococcus aureus. J Bacteriol 174, 4000–4006.
Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.
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0.05) from those for strain 10bT, as determined by ANOVA.
