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Sequencing libraries of bacterial communities of soil, rhizosphere and root endosphere were prepared according to the Illumina 16S Metagenomic Sequencing Library Preparation guide. Briefly, the V3-V4 regions of the 16S bacterial rRNA gene were amplified using a two-step PCR protocol with V3-V4 primers (For: 5-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG CCTACGGGNGGCWGCAG-3; Rev: 5-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG GACTACHVGGGTATCTAATCC-3) for the first PCR step and Illumina Nextera XT Index kit (Illumina Inc., San Diego, CA, USA) for the second PCR step. The first PCR step (amplicon PCR) was carried out to amplify the community microbial DNA using V3V4 primer sets with 2X KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Woburn, MA, USA) in a total volume of 25 l. The cycle conditions were as follows: initial cycle at 95C for 3 min, 25 cycles of denaturation at 95C for 30 sec, annealing at 55C for 30 sec and 72C for 30 sec with a final extension 72C for 5 minutes. The second PCR step (index PCR) was carried out to attach the dual indexes (N7xx and S5xx) and Illumina sequencing adapters using 2X KAPA HiFi HotStart ReadyMix in a total volume of 50ul. The PCR conditions were as follows: initial cycle at 95C for 3 min, 8 cycles at 95C for 30 sec, 55C for 30 sec and 72C for 30 sec with a final extension at 72C for 5 min. Amplicons were cleaned using Agencourt AMPure XP (Beckman Coulter Inc., Brea, CA, USA) magnetic beads. Libraries were validated with Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 bioanalyzer with the DNA 7500 kit (Agilent Technologies, Santa Clara, CA, USA) and quantified with qRT-PCR using KAPA library quantification kit (KAPA Biosystems, Woburn, MA, USA). Library was normalized and sequenced on an Illumina MiSeq (Illumina Inc., San Diego, CA, USA) instrument using the MiSeq reagent V2 chemistry kit.