Computational protocol: The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome

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Protocol publication

[…] Sequences were analyzed with the Qiime software version 6.0 (Caporaso et al., ). Replicates from sequencing of each treatment and habitat were bioinformatically pooled during the Qiime analysis for data evaluation. MID-, primer and adapter sequences were removed, length filtered (≥350 nt), quality filtered (score: 50), denoised, chloroplast removed and singletons adjusted. The cut-off level was set to 97% sequence identity. Chimeras were detected with Chimera Slayer and then removed. To compute alpha and beta diversity, the dataset was normalized to 5920 reads per sample. Ring-charts were created using the Krona software package version 2.2 (Ondov et al., ) and the profile network was constructed using Cytoscape version 3.0.2 (Shannon et al., ). Statistical tests based on the operational taxonomic units (OTUs) table were performed with the nonparametric ANOVA Kruskal Wallis test. This test is functionally an expansion of ANOVA to cases where the sample means are unequal and the distribution is not normal. […]

Pipeline specifications

Software tools QIIME, Krona
Application Phylogenetics
Organisms Homo sapiens, Bacillus velezensis FZB42, Rhizoctonia solani, Bacillus amyloliquefaciens