Microbial communities obtained from microcosms showing RDX degradation
Total genomic DNA samples were extracted from soil microorganisms that showed degradation of the amended labeled (15N or 13C) or unlabeled RDX. Total genomic DNA was also extracted from the initial soil and controls microcosms without any RDX added.  The samples were then subject to Illumina Amplicon sequencing. The V4 region of the 16S rRNA gene was amplified using a set of multiplex indexed primers based on the method of Caporaso et al. (2011). After amplification individual reactions were quantitated and a pool of equimolar amounts of each reaction was made. The pool was run on the Illumina MiSeq platform using a standard MiSeq paired end (2x250bp) flow cell and reagent cartridge following the manufacturer's instructions. The sequences were then assembled, processed for errors, chimeras etc using Mothur (kozhich et al. (2013)).