Microbiome Profiling from Soil Samples

Genomic Mini AX Bacteria+” (A&A Biotechnology, Gdynia, Poland) served for isolation of DNA from soil samples, while employing universal starters 1055F (5′-ACGGGCGGTGTGTAC-3′) and amplifying a fragment of the bacterial genes 16S rRNA and ITS. Detailed PCR settings were presented in our earlier papers [82 (link)]. Sequencing of genetic material on the basis of the hypervariable region V3–V4 of the gene rRNA and the ITS1 fragment was carried out on a sequencer Illumina MiSeq (Genomed S.A. Warsaw, Poland). Primers 341F (5′-CCTACGGGNGGCWGCAG-3′), 785R (5′-GACTACHVGGGTATCTAATCC-3′) (Bacteria) and ITS1FI2 (5′-GAACCWGCGGARGGATCA-3′), 5.8S (5′-CGCTGCGTTCTTCATCG-3′) (Fungi) were used for amplification of the selected region. Sequences of bacteria and fungi were deposited in the GenBank NCBI under the access numbers: https://www.ncbi.nlm.nih.gov/nuccore/?term=OP914644:OP916021[accn] (accessed on 4 December 2022), https://www.ncbi.nlm.nih.gov/nuccore/?term=OP897054:OP897145[accn] (accessed on 2 December 2022), https://www.ncbi.nlm.nih.gov/nuccore/?term=OP978693:OP979103[accn] (accessed on 14 December 2022).

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Borowik A., Wyszkowska J., Zaborowska M, & Kucharski J. (2023). Microbial Diversity and Enzyme Activity as Indicators of Permethrin-Exposed Soil Health. Molecules, 28(12), 4756.

Publication 2023

Genomic Mini AX Bacteria+”

16s rrna Bacteria Bacterial genes Fungi Genetic material Genomic Isolation Primers Rrna gene

Corresponding Organization : University of Warmia and Mazury in Olsztyn

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Variable analysis

independent variables

Soil samples

dependent variables

Sequencing of genetic material on the basis of the hypervariable region V3–V4 of the gene rRNA and the ITS1 fragment

control variables

Genomic Mini AX Bacteria+ protocol for DNA isolation
Universal starters 1055F (5′-ACGGGCGGTGTGTAC-3′) for amplification of a fragment of the bacterial genes 16S rRNA and ITS
Primers 341F (5′-CCTACGGGNGGCWGCAG-3′), 785R (5′-GACTACHVGGGTATCTAATCC-3′) (Bacteria) and ITS1FI2 (5′-GAACCWGCGGARGGATCA-3′), 5.8S (5′-CGCTGCGTTCTTCATCG-3′) (Fungi) for amplification of the selected region

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