Faecal/Soil Total DNA™ extraction kit (Zymo Research Corporation, CA, USA) was used to extract environmental DNA from ground root endosphere and rhizospheric soils according to manufacturer’s instructions and stored at − 20 °C prior to further analysis. For each sample, DNA was extracted in triplicates and pooled together. 16S rRNA gene fragments libraries preparation using 27F and 518R primer pairs, fused with MiSeq adapters and heterogeneity spacers was done according to protocol described by Ogola et al. [18 (link)]. Resultant libraries were sequenced by paired end (300 bp reads) sequencing v.3 chemistry along with its multiplex sample identifiers on the Illumina MiSeq Platform according to standard protocol.
Raw Fastq files from Illumina sequencing have been deposited at the NCBI sequence read archive (SRA) as BioProject ID PRJNA742387. The sequences were curated using the mothur v1.40.5 pipeline implemented in Nephele (v2.2.8) [19 (link)]. Sequences were assigned to operational taxonomic units (OTUs) using a dissimilarity cutoff = 0.03 and classified to representative microbial taxa against the nonredundant SILVA v132 ribosomal RNA database.
Raw Fastq files from Illumina sequencing have been deposited at the NCBI sequence read archive (SRA) as BioProject ID PRJNA742387. The sequences were curated using the mothur v1.40.5 pipeline implemented in Nephele (v2.2.8) [19 (link)]. Sequences were assigned to operational taxonomic units (OTUs) using a dissimilarity cutoff = 0.03 and classified to representative microbial taxa against the nonredundant SILVA v132 ribosomal RNA database.
Free full text: Click here
