For characterisation of microbial communities in all experiments, microbial DNA was extracted from each swab sample in a randomised order using a PowerSoil DNA Isolation kit (Qiagen) following the manufacturers protocol. DNA extracts were quantified using spectrophotometry (Nanodrop 1000) and stored at -20 °C until sequencing.
The extracted DNA samples were amplified with Polymerase Chain Reaction (PCR) using the 16 S rRNA gene primers 341 (F) (5’- CCTACGGGNGGCWGCAG-3’) and 805(R) – (5’-GACTACHVGGGTATCTAATCC-‘3), covering the V3-V4 regions of the bacterial and archaeal 16 S rRNA gene100 (link). The PCR conditions involved a pre-heating step to 95 °C for 3 min followed by 35 cycles of 95 °C for 15 s, 55 °C for 1 min and 73 °C for 30 s. Both positive (with known DNA sequence) and negative controls (nuclease-free water, control swabs) were used. The negative controls did not amplify DNA, suggesting no contamination on swabs/materials or during extraction and amplification. Agarose gel electrophoresis and Nanodrop 1000 were used to ensure the quantity and quality of the amplicons before they were sent for sequencing via the Illumina MiSeq 2000 platform at the Ramaciotti Centre for Genomics (UNSW, Sydney).
The extracted DNA samples were amplified with Polymerase Chain Reaction (PCR) using the 16 S rRNA gene primers 341 (F) (5’- CCTACGGGNGGCWGCAG-3’) and 805(R) – (5’-GACTACHVGGGTATCTAATCC-‘3), covering the V3-V4 regions of the bacterial and archaeal 16 S rRNA gene100 (link). The PCR conditions involved a pre-heating step to 95 °C for 3 min followed by 35 cycles of 95 °C for 15 s, 55 °C for 1 min and 73 °C for 30 s. Both positive (with known DNA sequence) and negative controls (nuclease-free water, control swabs) were used. The negative controls did not amplify DNA, suggesting no contamination on swabs/materials or during extraction and amplification. Agarose gel electrophoresis and Nanodrop 1000 were used to ensure the quantity and quality of the amplicons before they were sent for sequencing via the Illumina MiSeq 2000 platform at the Ramaciotti Centre for Genomics (UNSW, Sydney).
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