Similar protocols

Protocol publication

[…] s and figures is available in Additional file , and the approach is outlined in Additional file : Supplementary methods. Briefly, the OTU and taxonomy tables were filtered to exclude OTUs classified as eukaryotes, chloroplasts, and mitochondria. The OTU table was rarefied to 20,000 sequences per sample (Additional file : Supplementary methods, Figure S10), and the abundance of each OTU was expressed as percentages of the total number of counts in a sample. All statistical analyses were performed on log2 + 1 transformed data. All P values were adjusted for multiple comparisons with the false discovery rate (FDR) correction using the Benjamini-Hochberg method []. We made use of the R packages vegan v2.3-5 [], picante v1.6-2 [], and the Bioconductor package phyloseq v1.14 []., Detailed information regarding isolation, sequencing, and taxonomic assignment of bacteria isolates is available in Additional file : Supplementary methods., We isolated root-associated bacteria from two climate chamber experiments and from Trifolium individuals collected from the field site by plating serial dilutions of a root slurry onto flour medium agar [] plates amended with 10 μg mL−1 cycloheximide (to inhibit fungal growth; Sigma Aldrich, St. Louis, MO, USA). DNA extracted from single colony isolates was subjected to PCR using the primers 27F [] and 1401R [] and Sanger sequenced with 1401R as the sequencing primer by Microsynth AG (Balgach, Switzerland). These seq […]

Pipeline specifications

Software tools vegan, Picante, phyloseq
Diseases Disease
Chemicals Nitrogen