16S RNA profiling: groundwater
Total DNA was extracted from bacterial cells collected on each filter membrane following the method of The UltraCleanŽ Microbial DNA Isolation kit (MO BIO). DNA extracts were used to amplify 16S rRNA genes using bacterial 16S rRNA specific primers. Amplicons were purified via a SPRI bead clean-up step, quantitated by picogreen assay, normalized, pooled, and then sequenced on an Illumina Solexa instrument. The sequencing run resulted in ~100000 reads per sample with an average read length of 295 bp. Reads were filtered to retain those longer than 250 bp with an average quality score of greater than or equal to 30.