Bacterial and archaeal community composition were assessed by sequencing the 16S rRNA gene (bacteria and archaea) region. Soil samples for microbial community composition were homogenized in the field, with a subsample scooped into a 15-ml plastic tube to which a sucrose-lysis buffer was added. Samples were stored at -80°C and shipped to the University of New Mexico for analysis. Dual-index paired-end amplicon sequencing of 16S rRNA genes was performed using V6 universal bacterial primers 939F 50 TTG ACG GGG GCC CGC ACA AG-30 and 1492R 50-GTT TAC CTT GTT ACG ACT T-30 on an Illumina MiSeq. Raw sequence data was demultiplexed, binned by sample, and quality screened as described in Dowd et al. (2008). The Quantitative Insights into Microbial Ecology (QIIME) pipeline was used to analyze the 16S rRNA gene sequences. Unique 16S rRNA gene sequences or operational taxonomic units (OTUs) were identified by the 97% DNA identity criterion using UCLUST. A representative sequence was picked from each OTU and aligned using the PyNAST aligner and the Greengenes core set and given taxonomic assignments using the Ribosomal Database Classifier program.
Community analysis of the sequences were performed using QIIME (Caporaso et al. 2010) and mothur (Schloss et al. 2009) and statistical comparisons of the communities to each other and to environmental parameters were made in the vegan package (Oksanen et al. 2012) in R (R Development Core Team 2011).
