Metagenomic DNA Extraction and Sequencing

Concentrated cells from the CellTraps were centrifuged at 21 000 × g for 30 min prior to being re-suspended in 180 μL ATL buffer (Qiagen) and 20 μL proteinase K (20 mg mL⁻¹). The filters were removed from the falcon tubes, placed in 2 mL eppendorfs with 540 μL ATL buffer (Qiagen) and 60 μL proteinase K (20 mg mL⁻¹) added to them. Sample tubes from both methods were incubated at 55 °C for 30 min and DNA extraction and PCR amplification followed the same procedure as described in Pearman et al.^{16 (link)}. The primers used for amplification targeted the v3 and v4 regions of the 16S rRNA gene^{96 (link)} and the v4 region of the 18S rRNA gene^{97 (link)}. Subsequent to the PCR amplification (where a no negative control was also run) samples were cleaned and normalized using a SeqPrep Normalization plate prior to MiSeq library preparation. The library was prepared following the Illumina 16S metagenomic sequencing library preparation protocol. Before sequencing the samples were cleaned and normalized a second time and tagged samples were pooled for sequencing on a MiSeq sequencing platform at the King Abdullah University Core Laboratory. Raw reads were submitted to the NCBI SRA archive and can be accessed under the project accessions: SRP060785 and SRP081162.