Amplicon sequencing.

To distinguish between well-to-well contamination derived from DNA extraction and that derived from the PCR setup, each UCSD-processed DNA extraction plate (2 robot plates and 1 manual plate) was subjected to two separate triplicate PCRs, labeled PCRA or PCRB (Fig. 1b to ​tod).d). The mock community dilution plate and barcode testing plate were processed with a single triplicate PCR each. The EMP 16S rRNA V4 primers 515f and 806rB were used to amplify the samples. Equal concentrations of amplicons from each sample from all 8 plates were pooled and sequenced using the MiSeq platform (5, 13, 14). The 192 samples DNA extracted at Argonne were processed using the same EMP primers and method but on a separate MiSeq run. Amplicon data were uploaded to Qiita (41) and processed with Qiime 1.9.1 (42). Exact sequence tags from the first read (150 bp) were generated using the Deblur pipeline with default parameters as described previously (43).