DNeasy PowerMax Soil Kit (10)

Protocol tips

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	Follow manufacturer's instructions

Protocol tips
Follow manufacturer's instructions

Publication protocol

Soils tightly adhered to the plants’ roots were collected from Ventersdorp (F1), at 26°19′38″S and 26°53′18″E, and Mafikeng (F2), at 25°48′00″S and 25°38′21″E. Samples were collected from four points in each field (F1, GZ1 to GZ4; F2, AG1 to AG2). Soil samples were sieved and homogenized, and whole microbial DNA was extracted from 5 g of each sample using a DNeasy PowerMax soil kit (Qiagen, Denmark) following the manufacturer’s instructions. This study’s data sets are whole-metagenome shotgun-sequencing products at the Molecular Research Laboratory (MR DNA, Shallowater, TX, USA). Metagenomic DNA libraries were set using the Nextera DNA Flex library preparation kit (Illumina) according to the manufacturer’s guidelines. The initial DNA concentration was determined using the Qubit double-stranded DNA (dsDNA) high-sensitivity (HS) assay kit (Life Technologies), and samples were cleaned with a DNeasy PowerClean Pro cleanup kit (Qiagen). The samples were further subjected to simultaneous fragmentation, and adapter sequences were added and used in a limited-cycle PCR. After that, unique indices were added, and final library concentrations were determined using a Qubit dsDNA HS assay kit (Life Technologies), while the average size of the library was measured using an Agilent 2100 bioanalyzer. The libraries were pooled and diluted to 0.6 nM and paired-end sequenced for 300 cycles using the NovaSeq system (Illumina). Analysis and annotation of output data were performed in the metagenomics rapid annotation (MG-RAST) online server (2, 3) using default parameters. Following quality control (QC), sequences were annotated using the BLAT algorithm (4, 5) against the M5nr database (6), which offers nonredundant integration of numerous databases.

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Manufacturer protocol

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