Persistence Control SFA: RhizoGrid Indexed Sorghum Rhizosphere 16S rRNA
DNA concentrations were quantified using a Qubit 3.0 Fluorometer and normalized prior to amplification. The V3-V4 region of the 16S rRNA gene was targeted using a dual-indexed primer set (341F/785R) and amplified with Invitrogen Platinum Hot Start PCR Master Mix, using 10 ng of template DNA per reaction. PCRs were performed in triplicate across three thermocyclers to avoid bias, with pooled replicates subsequently quantified. Amplicons were pooled (100 ng per product), purified using AMPure XP beads, and diluted to 10 nM prior to sequencing. Libraries were sequenced at the UC Berkeley QB3 facility using the Illumina MiSeq platform (2  300 bp, v3 chemistry). DNA extraction was conducted using Quick-DNATM Fecal/Soil Microbe Miniprep Kit (D6010) and samples were prepared according to the kit protocol. 16S rRNA amplicon sequencing reads were processed using DADA2.