Computational protocol: Niche Filtering of Bacteria in Soil and Rock Habitats of the Colorado Plateau Desert, Utah, USA

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[…] USEARCH v8.0.1623 () was used to quality control and process the raw sequencing reads, with the following workflow to remove anomalous sequences. First, the forward and reverse paired-end reads were merged, and the merged reads with lengths outside 200–500 bp range or exceeding six homopolymers were removed by Mothur v1.36.1 (). Next, the sequences were subjected to Q score filtering to remove reads with maximum expected error > 1. Singleton reads were then removed.Representative sequences of the operational taxonomic units (OTUs; Supplementary Table ) were taxonomically assigned using the RDP classifier () implemented in QIIME v1.9.1 (). Greengenes release 13_8 () was used as the reference taxonomic database. The OTU table was rarefied to 16,058 sequences per sample to remove sample heterogeneity; rarefaction analysis indicated that sequencing depth was sufficient to identify the majority of OTUs within each community (Supplementary Figure ). Rarefaction, alpha and beta diversity analyses were performed in QIIME (). Permutational multivariate analysis of variance (PERMANOVA) on the community weighted UNIFRAC distance matrix was performed with the adonis function in the R package “vegan” v2.3.3 (); 1000 replicate permutations were made. Differential abundance analysis was performed with DESeq2 () as implemented in the R package “phyloseq” v1.15.2 (). All sequence data is available under the study accession number PRJEB15188. […]

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