Creek water post-rain, input
A 1000 ml water sample was collected from a creek 25 meters downstream from a sedimentation pond used for primary passive treatment of ground water run-off. A 100 ml aliquot was filtered over a 0.2 µm Nalgene sterile analytical filter unit (Thermo Scientific) prior to DNA extraction with the PowerWater DNA Isolation Kit (MO BIO Laboratories). A 150 ng aliquot of the DNA was subjected to the DpnI pull-down assay.  The input, unbound, and bound/eluted fractions were used to prepare sequencing libraries.  Library preparation and sequencing   The Nextera DNA Sample Preparation Kit (Illumina, San Diego, CA) was used to prepare libraries from input, unbound, and bound/eluted fractions from DpnI pulldown assays. Manufacturer’s instructions were followed for the library preparation except for recommended number of PCR cycles, which were varied according to the amount of DNA. For the synthetic mixture, they were as follows: Input – 7 cycles, DpnI bound – 10 cycles, DpnI unbound – 7 cycles. Libraries were sequenced following the manufacturer’s instructions for the HiSeq 2500 Rapid Run mode to obtain 50 nucleotide readlengths.