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  • 1
    Electronic Resource
    Electronic Resource
    Characterization of nitrogen-fixing Paenibacillus species by polymerase chain reaction–restriction fragment length polymorphism analysis of part of genes encoding 16S rRNA and 23S rRNA and by multilocus enzyme electrophoresis (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 222 (2003), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Forty-two strains representing the eight recognized nitrogen-fixing Paenibacillus species and 12 non-identified strains were examined by restriction fragment length polymorphism (RFLP) analysis of part of 16S and 23S rRNA genes amplified by polymerase chain reaction (PCR). Eleven different 16S rDNA genotypes were obtained from the combined data of RFLP analysis with four endonucleases and they were in agreement with the established taxonomic classification. Only one group of unclassified strains (Group I) was assigned in a separate genotype, suggesting they belong to a new species. Using the 23S PCR–RFLP method only six genotypes were detected, showing that this method is less discriminative than the 16S PCR–RFLP. Using the multilocus enzyme electrophoresis (MLEE) assay, the 48 strains tested could be classified into 35 zymovars. The seven enzymatic loci tested were polymorphic and the different profiles obtained among strains allowed the grouping of strains into 10 clusters. The PCR–RFLP methods together with the MLEE assay provide a rapid tool for the characterization and the establishment of the taxonomic position of isolates belonging to this nitrogen-fixing group, which shows a great potentiality in promoting plant growth.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0378-1097(03)00300-8
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  • 2
    Electronic Resource
    Electronic Resource
    Assessment of the diversity of Paenibacillus species in environmental samples by a novel rpoB-based PCR-DGGE method (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 53 (2005), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: A specific PCR system based on the gene encoding the RNA polymerase beta subunit, rpoB, was developed for amplification and denaturing gradient gel electrophoresis (DGGE) fingerprinting of Paenibacillus communities in environmental samples. This gene has been previously proven to be a powerful identification tool for the discrimination of species within the genus Paenibacillus and could avoid the limitations of 16S rRNA-based phylogenetic analysis. Initially, the PCR system based on universal rpoB primers were used to amplify DNAs of different Paenibacillus species. A new reverse primer (rpoBPAEN) was further designed based on an insertion of six nucleotides in the Paenibacillus sequences analyzed. This semi-nested PCR system was evaluated for specificity using DNAs isolated from 27 Paenibacillus species belonging to different 16S rRNA-based phylogenetic groups and seven non-Paenibacillus species. The non-Paenibacillus species were not amplified using this PCR approach and one group of Paenibacillus species consisting of strains without the six-base insert also were not amplified; these latter strains were found to be distinct based on 16S rRNA gene phylogeny. In addition, a clone library was generated from the rpoB fragments amplified from two Brazilian soil types (Cerrado and Forest) and all 62 clones sequenced were closely related to one of the 22 sequences from Paenibacillus previously obtained in this study. To assess the diversity of Paenibacillus species in Cerrado and Forest soils and in the rhizosphere of different cultivars of maize, a PCR-DGGE system was used. The Paenibacillus DGGE fingerprints showed a clear distinction between communities of Paenibacillus in Forest and Cerrado soils and rhizosphere samples clustered along Cerrado soil. Profiles of cultivars CMS22 and CMS36 clustered together, with only 53% of similarity to CMS11 and CMS04. The results presented here demonstrate the potential use of the rpoB-based Paenibacillus-specific PCR-DGGE method for studying the diversity of Paenibacillus populations in natural environments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2005.01.017
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  • 3
    Electronic Resource
    Electronic Resource
    Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 49 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The aim of this study was to analyse the effect of oil contamination and biostimulation (soil pH raise, and nitrogen, phosphate and sulphur addition) on the diversity of a bacterial community of an acidic Cambisol under Atlantic Forest. The experiment was based on the enumeration of bacterial populations and hydrocarbon degraders in microcosms through the use of conventional plating techniques and molecular fingerprinting of samples directly from the environment. PCR followed by denaturing gradient gel electrophoresis (DGGE) was used to generate microbial community fingerprints employing 16S rRNA gene as molecular marker. Biostimulation led to increases of soil pH (to 7.0) and of the levels of phosphorus and K, Ca, and Mg. Oil contamination caused an increase in soil organic carbon (170–190% higher than control soil). Total bacterial counts were stable throughout the experiment, while MPN counts of hydrocarbon degraders showed an increase in the biostimulated and oil-contaminated soil samples. Molecular fingerprinting performed with 16S rRNA gene PCR and DGGE analysis revealed stable patterns along the 360 days of experiment, showing little change in oil-contaminated microcosms after 90 days. The DGGE patterns of the biostimulated samples showed severe changes due to decreases in the number of bands as compared to the control samples as from 15 days after addition of nutrients to the soil. Results obtained in the present study indicate that the addition of inorganic compounds to soil in conjunction with oil contamination has a greater impact on the bacterial community than oil contamination only.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.04.007
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  • 4
    Electronic Resource
    Electronic Resource
    Bacillus nitrogen fixers from Brazilian soils (1983)
    Springer
    Plant and soil 70 (1983), S. 243-255 
    Details
    ISSN: 1573-5036
    Keywords: Acetylene reduction ; Bacillius ; Identification ; Soil ; Spore enumeration
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Five different Brazilian soils were examined for the incidence of Bacillus nitrogen fixers. These counts were set in relation to the total spore count, and the number of facultative anaerobic spores. Twenty-four Bacillus strains were isolated using media lacking a nitrogen source, identified and their acetylene-reducing ability was determined. Eighteen of these strains were identified asB. polymyxa, and the other 6 were related to this species, but were different in some taxonomical tests. Of the 24 isolated strains, only 13 reduced acetylene; similarly, only 3 out of 9B. polymyxa reference strains were able to reduce acetylene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02374784
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    Bacillus polymyxa bacteriophages from Brazilian soils (1984)
    Springer
    Antonie van Leeuwenhoek 50 (1984), S. 39-51 
    Details
    ISSN: 1572-9699
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Ten phages of Bacillus polymyxa were isolated from four different Brazilian soils. All were dsDNA-containing phages belonging to Bradley types A and B. Data obtained from electron microscopy and tests of resistance against physical and chemical agents showed that the isolates could be distributed among six different groups. Host range data were in agreement with this classification. When tested against 88 strains of 18 Bacillus species, these phages only infected B. polymyxa strains, thus revealing specificity for this species. Three phage groups lysed all 42 available B. polymyxa strains and are suggested for use in rapid identification of this species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00404906
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  • 6
    Electronic Resource
    Electronic Resource
    Identification of Bacillus azotofixans using API tests (1986)
    Springer
    Antonie van Leeuwenhoek 52 (1986), S. 403-409 
    Details
    ISSN: 1572-9699
    Keywords: Identification ; Bacillus azotofixans
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The identification of Bacillus azotofixans strains using API tests is described. Twenty-two strains were studied according to their fermentation pattern on 49 different carbohydrates. A profile of the B. azotofixans type strain is presented, together with an average profile of all strains tested. The fermentation pattern for B. azotofixans is also compared to those of the closely similar species B. polymyxa and B. macerans. These profiles may be useful for the identification of new strains.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00393468
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  • 7
    Electronic Resource
    Electronic Resource
    Evaluation of Biolog system for identification of strains of Paenibacillus azotofixans (1997)
    Springer
    Antonie van Leeuwenhoek 71 (1997), S. 195-200 
    Details
    ISSN: 1572-9699
    Keywords: Biolog system ; Paenibacillus azotofixans ; identification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Biolog system was evaluated for the identification of strains of Paenibacillus azotofixans as no data concerning this species were in the list of Bacillus currently identified using Biolog data base. The P. azotofixans type strain P3L5 was first tested with the results recorded manually or using the automatic plate reader. In both cases, P3L5 utilized 22 carbon sources and when the results obtained were compared to data of Biolog software (Release 3.50), P3L5 was identified as B. azotoformans with a similarity coefficient of 0.913 (data recorded manually) and of 0.791 (data recorded automatically). Metabolic profiles of P3L5 were also compared after readings of 4 and 24 h using the computer-driven automatic plate reader. No significant difference was observed in both cases and P3L5 was identified again as B. azotoformans with indices of similarity considered only for ‘excellent identification’. Besides P3L5, other 15 P. azotofixans strains were tested with the Biolog system and all were identified as B. azotoformans with similarity coefficients varying from 0.511 to 0.927. Phenotypic and genetic characteristics of B. azotoformans were compared to those described for P. azotofixans to explain the misidentification of the latter species. We could conclude that these two species are quite different and that data of Biolog software are from P. azotofixans and not from B. azotoformans.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1000128314946
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  • 8
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    A communal catalogue reveals Earth’s multiscale microbial diversity (2017)
    Nature Research
    In:  Nature, 551 (7681). pp. 457-463.
    Details
    Publication Date: 2020-02-06
    Description: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/nature24621
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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