Bacterial Community Profiling by SSCP

Fingerprinting by SSCP analysis was carried out as described by Schwieger & Tebbe38 (link). Bacterial 16S rRNA gene sequences were PCR-amplified using the eubacterial primer pair Unibac-II-515f and Unibac-II-927r^P. Separation and analysis were performed according to Köberl et al.39 (link). Comparisons of generated bacterial community profiles were performed using GelCompar II 5.1 (Applied Maths, Kortrijk, Belgium). Cluster analyses were performed with the following settings: dendrogram type: unweighted pair group method with arithmetic mean (UPGMA); similarity coefficient: curve based: Pearson correlation; position tolerances: optimisation: 0.2%, position tolerance: 1%. Multidimensional scaling (MDS) ordination plots were constructed based on the Pearson similarity matrices. These matrices were additionally subjected to significance tests of pair-wise similarities by applying permutation analyses (p ≤ 0.01) using the permtest package of R statistics 3.2.0 (The R Foundation for Statistical Computing, Vienna, Austria) with 10⁵ random permutations of sample elements40 (link)41 . Excised and re-amplified DNA fragments were sequenced at LGC Genomics (Berlin, Germany).

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Nimusiima J., Köberl M., Tumuhairwe J.B., Kubiriba J., Staver C, & Berg G. (2015). Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure. Scientific Reports, 5, 18078.

Publication 2015

GelCompar II 5.1

16s rrna Bacterial Bacterial gene Primer Sscp Tolerance

Corresponding Organization :

Other organizations : National Agricultural Research Organisation, Graz University of Technology, Makerere University, Institut Agro Montpellier

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Variable analysis

independent variables

Fingerprinting by SSCP analysis
Bacterial 16S rRNA gene sequences were PCR-amplified using the eubacterial primer pair Unibac-II-515f and Unibac-II-927r

dependent variables

Bacterial community profiles

control variables

Separation and analysis were performed according to Köberl et al.39
Cluster analyses were performed with the following settings: dendrogram type: unweighted pair group method with arithmetic mean (UPGMA); similarity coefficient: curve based: Pearson correlation; position tolerances: optimisation: 0.2%, position tolerance: 1%
Multidimensional scaling (MDS) ordination plots were constructed based on the Pearson similarity matrices
Permutation analyses (p ≤ 0.01) using the permtest package of R statistics 3.2.0 with 10^5 random permutations of sample elements

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