Supplementary Information 2 – Data tables, Q2Pipe options, and R scripts for statistical analyses

This supplementary material file describes the parameters used in the bioinformatics analyses performed with QIIME 2 within the Q2Pipe workflow (v0.95; https://github.com/NRCan/Q2Pipe), as well as the R scripts for the statistical analyses of microbial data performed in RStudio (v4.4.2) supporting our study: "Tree tissues and species traits modulate the microbial methane-cycling communities of the tree phyllosphere" (associated preprint: DOI:10.21203/rs.3.rs-6066438/v1). This data analysis workflow was developed to investigate the structure of methane-cycling microbial communities of tree phyllosphere using 16S rRNA gene metabarcoding data.Included are the options file for the Q2Pipe pipeline, rarefaction curve outputs showing the number of features across sequencing depths, and scripts used for alpha- and beta-diversity analyses, compositional analyses of methane-cycling microbial communities, and linear regression models describing the relative abundance of methane-cycling microorganisms.