DNA Extraction from Filters and Sediments

DNA was extracted as described previously for filters (Orsi et al., 2015 (link)) and sediments (Coskun et al., 2018 (link)). DNA from the sediments was performed exactly as described previously (Coskun et al., 2018 (link)). For the filters, some modifications to the original DNA extraction protocol (Orsi et al., 2015 (link)) were made. For the filters, the silica bead contents from four 2 mL Lysing Matrix E tubes (MP Biomedicals, Solon, OH, USA) was poured into a 15-ml falcon tube containing the filter 4 ml of a sterile-filtered sucrose ethylene-diaminetetraacetic lysis buffer (0.75 M sucrose, 0.05 M Tris-Base, 0.02 M ethylenediaminetetraacetic, 0.4 M NaCl, 4 ml 10% sodium dodecyl sulfate, and pH 9.0) was added to the tubes and then bead beating was performed for 40 s using a Fast-Prep 5G homogenizer (MP Biomedicals, OH, USA) at a speed of 6 m/s. Samples were subsequently heated for 2 min at 99°C. After heating, 25 ml of 20 mg/ml proteinase K was added, and tubes were incubated at 55°C overnight with constant gentle rolling in a Bambino oven. DNA was extracted and purified from the lysate using the DNeasy Blood and Tissue Kit (Qiagen). Extracted DNA was quantified fluorometrically using a Qubit 3.0 Fluorometer (Invitrogen, Eugene, OR, USA).