Genematrix soil dna purification kit

Total DNA was extracted from 0.5 g soil samples using a GeneMATRIX Soil DNA Purification Kit (Eur_x, Poland) as described in the manufacturer's instruction. The 16S rRNA gene fragment was amplified using the primers (GC-clamp)-F338 and R518 (Muyzer et al., 1993 (link)). Detailed information about this procedure was described in a previous paper (Cycon et al., 2013 (link)). The electrophoresis of the amplification products was performed in 8 % (w/v) polyacrylamide gel (37.5:1 acrylamide:bis-acrylamide) in the presence of a linear denaturing gradient that ranged from 40 to 70 % using a DCode Mutation Detection System (Bio-Rad, USA). In turn, a G BOX F3 System (Syngene, UK) was used to visualize the patterns of the bands that were obtained. Detailed information about the DGGE procedure was described in a previous paper (Cycon et al., 2016 (link)). The band patterns that were obtained from the DGGE analysis were analyzed using BioNumerics software ver. 7.5 (Applied Math, Belgium). The unweighted pair-group method and the arithmetic averages (UPGMA) were used to construct the phylogenic dendrograms. The biodiversity of a soil bacterial community was expressed as the Shannon-Wiener index (H'), richness (Rs) and evenness (Eh), which were calculated using the equations that were described in a previous paper (Cycon et al., 2013 (link)).

Pseudomonas sp. OF001 and Rubrivivax sp. A210 were obtained from the culture collection of the Laboratory of Environmental Microbiology from the TU Berlin, Germany [2 (link)]. Bacteria were routinely cultivated in a medium that was originaly developed for Leptothrix strains [117 ], which was modified by our research group and is known as LSM2.
Cells from a pure, fresh 50 mL liquid culture from each strain were harvested by centrifugation at 15,000 x g for 3 min and washed three times with sterile Milli Q water under sterile conditions. Total genomic DNA was extracted using the GeneMATRIX Soil DNA Purification Kit (EUR_X Gdańsk, Poland) following the manufacturer’s instructions. Quality and quantity of the extracted DNA was determined using QubitTM fluorometric quantitation and NanoDrop 2000 (both Thermo Fisher Scientific, Bremen, Germany).