rpoD amplicon sequencing of fluorescent pseudomonads: Categorized by interaction with B. subtilis in pellicle
A library of 720 fluorescent Pseudomonas isolates were categorized by their interaction with B. subtilis DK1042, and cells were pooled by equal cell abundance in each category. gDNA was extracted with a EURx Bacterial & Yeast Genomic DNA Purification Kit, and the rpoD gene was amplified with PCR using barcoded primers (PsEG30F and PsEG790R), and the Ampliqon TEMPase Hotstart polymerase. DNA purity and concentration were assessed on a DeNovix spectrophotometer and a Qubit fluorometer, respectively. 360 ng barcoded amplicons from each sample were pooled and sequenced on the MiSeq PE300 platform using the MiSeq Reagent Kit V3(600-cycle). Reads were demultiplexed with CutAdapt.