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Bacteria Collection: Paenibacillus polymyxa

NCTC Number: NCTC 10343
Current Name: Paenibacillus polymyxa
Original Strain Reference: Kluyver
Other Collection No: ATCC 842; BUCSAV 162; CCM 1459; DSM 36; JCM 2507; LMG 13294; NCIB 8158
Previous Catalogue Name: Bacillus polymyxa
Type Strain: Yes
Family: Paenibacillaceae
Hazard Group (ACDP): 2
Release Restrictions: Terms & Conditions of Supply of Microbial Pathogens: Safety
Conditions for growth on solid media: Nutrient agar, 24-48 hours, 37°C, aerobic
Conditions for growth on liquid media: nutrient broth,37, facultative anaerobe
Whole Genome Sequence: http://www.ebi.ac.uk/ena/data/view/ERS1247825
16S rRNA Gene Sequence: >gb|AJ320493|DSM 36|Paenibacillus polymyxa partial 16S rRNA gene, strain DSM 36T.| ggctcaggacgaacg... >gb|U60659|DSM 36 (TYPE STRAIN)|Paenibacillus polymyxa 16S ribosomal RNA gene, partial sequence.| caggtcttgacatcc... >gb|U60658|DSM 36 (TYPE STRAIN)|Paenibacillus polymyxa 16S ribosomal RNA gene, partial sequence.| caggtcttgacatcc... >gb|U60657|DSM 36 (TYPE STRAIN)|Paenibacillus polymyxa 16S ribosomal RNA gene, partial sequence.| caggtcttgacatcc... >gb|U60656|DSM 36 (TYPE STRAIN)|Paenibacillus polymyxa 16S ribosomal RNA gene, partial sequence.| caggtcttgacatcc... >gb|U60655|DSM 36 (TYPE STRAIN)|Paenibacillus polymyxa 16S ribosomal RNA gene, partial sequence.| caggtcttgacatcc... >gb|U60654|DSM 36 (TYPE STRAIN)|Paenibacillus polymyxa 16S ribosomal RNA gene, partial sequence.| caggtcttgacatcc... >gb|X57308|DSM 36|B.polymyxa 16SrRNA.| ttaatggagagtttg... >gb|U36234|ATCC 842|Bacillus polymyxa 23S large subunit ribosomal RNA gene, partialsequence.| cttaggaccgtaata...
23S rRNA Gene Sequence: >gb|U36234|ATCC 842|Bacillus polymyxa 23S large subunit ribosomal RNA gene, partialsequence.| cttaggaccgtaata...
Bibliography: SMITH N R ET AL 1964 J GEN MICROBIOL 34 269
Extended Bibliography: showhide Show bibliography
Ref #: 66901
Author(s): Nubel,U.;Engelen,B.;Felske,A.;Snaidr,J.;Wieshuber,A.;Amann,R.I.;Ludwig,W.;Backhaus,H.
Journal: J Bacteriol
Title: Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis
Volume: 178
Page(s): 5636-43
Year: 1996
Keyword(s): GENBANK/U60654 GENBANK/U60655 GENBANK/U60656 GENBANK/U60657 GENBANK/U60658 GENBANK/U60659 Bacillus/*genetics Blotting, Southern Cloning, Molecular DNA, Bacterial/*genetics DNA, Ribosomal/*genetics Electrophoresis, Polyacrylamide Gel/methods *Genetic Heterogeneity Molecular Sequence Data Nucleic Acid Conformation RNA, Ribosomal, 16S/*genetics Sequence Analysis, DNA Species Specificity Temperature
Remarks: Sequence heterogeneities in 16S rRNA genes from individual strains of Paenibacillus polymyxa were detected by sequence-dependent separation of PCR products by temperature gradient gel electrophoresis (TGGE). A fragment of the 16S rRNA genes, comprising variable regions V6 to V8, was used as a target sequence for amplifications. PCR products from P. polymyxa (type strain) emerged as a well-defined pattern of bands in the gradient gel. Six plasmids with different inserts, individually demonstrating the migration characteristics of single bands of the pattern, were obtained by cloning the PCR products. Their sequences were analyzed as a representative sample of the total heterogeneity. An amount of 10 variant nucleotide positions in the fragment of 347 bp was observed, with all substitutions conserving the relevant secondary structures of the V6 and V8 regions in the RNA molecules. Hybridizations with specifically designed probes demonstrated different chromosomal locations of the respective rRNA genes. Amplifications of reverse-transcribed rRNA from ribosome preparations, as well as whole-cell hybridizations, revealed a predominant representation of particular sequences in ribosomes of exponentially growing laboratory cultures. Different strains of P. polymyxa showed not only remarkably differing patterns of PCR products in TGGE analysis but also discriminative whole-cell labeling with the designed oligonucleotide probes, indicating the different representation of individual sequences in active ribosomes. Our results demonstrate the usefulness of TGGE for the structural analysis of heterogeneous rRNA genes together with their expression, stress problems of the generation of meaningful data for 16S rRNA sequences and probe designs, and might have consequences for evolutionary concepts.
URL: 8824607
Ref #: 66819
Author(s): da Mota,F.F.;Gomes,E.A.;Paiva,E.;Rosado,A.S.;Seldin,L.
Journal: Lett Appl Microbiol
Title: Use of rpoB gene analysis for identification of nitrogen-fixing Paenibacillus species as an alternative to the 16S rRNA gene
Volume: 39
Page(s): 34-40
Year: 2004
Keyword(s): Bacillaceae/*classification/genetics *Bacterial Typing Techniques DNA, Bacterial/analysis DNA-Directed RNA Polymerases/*genetics Genes, rRNA Molecular Sequence Data *Nitrogen Fixation Phylogeny Plant Roots/microbiology RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA Soil Microbiology Zea mays
Remarks: AIM: To avoid the limitations of 16S rRNA-based phylogenetic analysis for Paenibacillus species, the usefulness of the RNA polymerase beta-subunit encoding gene (rpoB) was investigated as an alternative to the 16S rRNA gene for taxonomic studies. METHODS AND RESULTS: Partial rpoB sequences were generated for the type strains of eight nitrogen-fixing Paenibacillus species. The presence of only one copy of rpoB in the genome of P. graminis strain RSA19(T) was demonstrated by denaturing gradient gel electrophoresis and hybridization assays. A comparative analysis of the sequences of the 16S rRNA and rpoB genes was performed and the eight species showed between 91.6-99.1% (16S rRNA) and 77.9-97.3% (rpoB) similarity, allowing a more accurate discrimination between the different species using the rpoB gene. Finally, 24 isolates from the rhizosphere of different cultivars of maize previously identified as Paenibacillus spp. were assigned correctly to one of the nitrogen-fixing species. CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: The data obtained in this study indicate that rpoB is a powerful identification tool, which can be used for the correct discrimination of the nitrogen-fixing species of agricultural and industrial importance within the genus Paenibacillus.
URL: 15189285
Ref #: 22221
Author(s): Rossler,D.;Ludwig,W.;Schleifer,K.H.;Lin,C.;McGill,T.J.;Wisotzkey,J.D.;Jurtshuk P,J.r.;Fox,G.E.
Journal: Syst Appl Microbiol
Title: Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies
Volume: 14
Page(s): 266-9
Year: 1995
Keyword(s): Bacillus/*classification/genetics Bacillus stearothermophilus/classification/genetics Bacillus subtilis/classification/genetics Base Sequence DNA, Bacterial/genetics *Phylogeny RNA, Bacterial/classification/*genetics RNA, Ribosomal, 16S/classification/*genetics Sequence Alignment *Sequence Homology, Nucleic Acid
Remarks: Comparative sequence analysis of 16S ribosomal (r)RNAs or DNAs of Bacillus alvei, B. laterosporus, B. macerans, B. macquariensis, B. polymyxa and B. stearothermophilus revealed the phylogenetic diversity of the genus Bacillus. Based on the presently available data set of 16S rRNA sequences from bacilli and relatives at least four major "Bacillus clusters" can be defined: a "Bacillus subtilis cluster" including B. stearothermophilus, a "B. brevis cluster" including B. laterosporus, a "B. alvei cluster" including B. macerans, B. maquariensis and B. polymyxa and a "B. cycloheptanicus branch".
URL: 11538306
Ref #: 12306
Author(s): Rossler,D.;Ludwig,W.;Schleifer,K.H.;Lin,C.;McGill,T.J.;Wisotzkey,J.D.;Jurtshuk P,J.r.;Fox,G.E.
Journal: Syst Appl Microbiol
Title: Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies
Volume: 14
Page(s): 266-9
Year: 1995
Keyword(s): Bacillus/*classification/genetics Bacillus stearothermophilus/classification/genetics Bacillus subtilis/classification/genetics Base Sequence DNA, Bacterial/genetics *Phylogeny RNA, Bacterial/classification/*genetics RNA, Ribosomal, 16S/classification/*genetics Sequence Alignment *Sequence Homology, Nucleic Acid Support, Non-U.S. Gov't Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S.
Remarks: Comparative sequence analysis of 16S ribosomal (r)RNAs or DNAs of Bacillus alvei, B. laterosporus, B. macerans, B. macquariensis, B. polymyxa and B. stearothermophilus revealed the phylogenetic diversity of the genus Bacillus. Based on the presently available data set of 16S rRNA sequences from bacilli and relatives at least four major "Bacillus clusters" can be defined: a "Bacillus subtilis cluster" including B. stearothermophilus, a "B. brevis cluster" including B. laterosporus, a "B. alvei cluster" including B. macerans, B. maquariensis and B. polymyxa and a "B. cycloheptanicus branch".
URL: 95609108
Ref #: 13713
Author(s): Nubel,U.;Engelen,B.;Felske,A.;Snaidr,J.;Wieshuber,A.;Amann,R.I.;Ludwig,W.;Backhaus,H.
Journal: J Bacteriol
Title: Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis
Volume: 178
Page(s): 5636-43
Year: 1996
Keyword(s): GENBANK/U60654 GENBANK/U60655 GENBANK/U60656 GENBANK/U60657 GENBANK/U60658 GENBANK/U60659 Bacillus/*genetics Blotting, Southern Cloning, Molecular Comparative Study DNA, Bacterial/*genetics DNA, Ribosomal/*genetics Electrophoresis, Polyacrylamide Gel/methods *Genetic Heterogeneity Molecular Sequence Data Nucleic Acid Conformation RNA, Ribosomal, 16S/*genetics Sequence Analysis, DNA Species Specificity Support, Non-U.S. Gov't Temperature
Remarks: Sequence heterogeneities in 16S rRNA genes from individual strains of Paenibacillus polymyxa were detected by sequence-dependent separation of PCR products by temperature gradient gel electrophoresis (TGGE). A fragment of the 16S rRNA genes, comprising variable regions V6 to V8, was used as a target sequence for amplifications. PCR products from P. polymyxa (type strain) emerged as a well-defined pattern of bands in the gradient gel. Six plasmids with different inserts, individually demonstrating the migration characteristics of single bands of the pattern, were obtained by cloning the PCR products. Their sequences were analyzed as a representative sample of the total heterogeneity. An amount of 10 variant nucleotide positions in the fragment of 347 bp was observed, with all substitutions conserving the relevant secondary structures of the V6 and V8 regions in the RNA molecules. Hybridizations with specifically designed probes demonstrated different chromosomal locations of the respective rRNA genes. Amplifications of reverse-transcribed rRNA from ribosome preparations, as well as whole-cell hybridizations, revealed a predominant representation of particular sequences in ribosomes of exponentially growing laboratory cultures. Different strains of P. polymyxa showed not only remarkably differing patterns of PCR products in TGGE analysis but also discriminative whole-cell labeling with the designed oligonucleotide probes, indicating the different representation of individual sequences in active ribosomes. Our results demonstrate the usefulness of TGGE for the structural analysis of heterogeneous rRNA genes together with their expression, stress problems of the generation of meaningful data for 16S rRNA sequences and probe designs, and might have consequences for evolutionary concepts.
URL: 96421990
Ref #: 1300
Author(s): Skerman,V.B.D.;McGowan,V.;Sneath,P.H.A.(ed)
Journal: Int. J. Syst. Bacteriol.
Title: Approved Lists of Bacterial Names.
Volume: 30
Page(s): 225-420
Year: 1980
Ref #: 2277
Author(s): Frommer,W.etal.
Title: Inhibitors, obtained from bacilli, for glycoside hydrolases.
Ref #: 2478
Author(s): Birnbaum,A.;etal.
Journal: Lebensm.- Wiss. Technol.
Title: Beitrag zur enzymatischen Bestimmung der Galakturonsäure (GA).
Volume: 12
Page(s): 231-233
Year: 1979
Ref #: 3768
Author(s): Fahmy,F.;Flossdorf,J.;Claus,D.
Journal: System. Appl. Microbiol.
Title: The DNA base composition of the type strains of the genus Bacillus.
Volume: 6
Page(s): 60-65
Year: 1985
Ref #: 4712
Author(s): Nakamura,L.K.
Journal: Int. J. Syst. Bacteriol.
Title: Bacillus polymyxa (Prazmowski) Mace 1889 deoxyribonucleic acid relatedness and base composition.
Volume: 37
Page(s): 391-397
Year: 1987
Ref #: 5192
Journal: Int. J. Syst. Bacteriol.
Title: Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 51.
Volume: 44
Page(s): 852
Year: 1994
Ref #: 5201
Author(s): Ash,C.;Priest,F.G.;Collins,M.D.
Journal: Antonie van Leeuwenhoek J. Microbiol.
Title: Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test.
Volume: 64
Page(s): 253-260
Year: 1993
Ref #: 6615
Author(s): Heyndrickx,M.;Vandermeulebroecke,K.;Kersters,K.;DeVos,P.;Logan,N.A.;Aziz,M.A.;Ali,N.;Berkeley,R.C.W.
Journal: Int. J. Syst. Bacteriol.
Title: 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 description of
Volume: 46
Page(s): 988-1003
Year: 1996
Data: (ATCC 842, NCIB 8158) Type Strain / T. Gibson, Edinburgh in 1963 / Smith, N. R. et al. (1964) J. gen. Microbiol. 34, 269
Accession Date: 01/01/1963
History: EDINBURGH SCHOOL OF AGRICULTURE
Authority: (Prazmowski 1880) Ash et al. 1994
Depositor: GIBSON T
Taxonomy: TaxLink: S425 (Bacillus polymyxa) - Date of change: 5/02/2003
Biosafety Responsibility: It is the responsibility of the customer to ensure that their facilities comply with biosafety regulations for their own country

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The Culture Collections hold cell cultures, bacteria, fungi and virus strains from worldwide sources. Our scientists ensure that the identification of the cultures is correct and they remain unchanged from when they are first deposited with the Collection. Nevertheless, some of the data we provide about the cultures is supplied by the person depositing the strains and, although we have multiple checking procedures in place, we cannot always verify all their data. Please note that the Culture Collections cannot be held responsible for any inaccuracies in the data provided by the depositors.

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