title: 16S metagenome; root vegetables
design: DNA was extracted using a RTPBacteria DNA Mini Kit (Stratec Biomedical Systems, Germany) according to the protocol, with one additional step:  the cells were lysed by bead beating with Zirconia/Silica beads (Biospec Products, USA): 0.1 mm  0.5 g with FastPrep-24 (MP Biomedicals, USA) at 4 m/s for 3 x 60 seconds. The V3-V4 region of the 16S rRNA gene was amplified using primers F341ad (3- CCAGACTCCTACGGGAGGCAG -5)(Sakai et al. 2004), R783ad (3-ACCMGGGTATCTAATCCKG-5) using Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific, USA) and approximately 20 ng of DNA in a 20 l reaction mixture. The PCR reaction was carried out at 98C for 30 s followed by 20 cycles each of 98C for 10 s, 50C for 30 s, and 72C for 30 s, followed by 5 min at 72C. PCR amplifications were performed in triplicate and then pooled. The pooled PCR products were cleaned using an UltraClean PCR Clean-Up Kit (MoBio, USA), and both the quantity and quality of DNA was determined spectrophotometrically (NanoDrop 2000c). DNA sequencing was carried out using the MiSeq (Illumina PE500) (San Diego, USA).