title: 16S rRNA gene sequencing of oil-degrading community in lab enrichment
design: At the end of the incubations the adsorbents with oil-associated biofilm were transferred to a 1.5 ml Eppendorf tube while the cells in the medium were collected by centrifugation at 13000 rpm for 5 min. Both the adsorbents and the cell pellet were stored at -80C until further processing.  DNA was extracted using the method described by Lever et al. (2005) with the following modification for optimized extraction efficiency as determined experimentally for our samples. A 0.5% Triton X-100 lysis solution was used that resulted in a 9-18% higher DNA yield. The DNA concentration was determined with the Quant-IT dsDNA High-sensitivity assay kit (Thermo Fisher scientific) and a Qubit Fluorometer (Thermo Fisher scientific).  The bacterial 16S rRNA gene copies were quantified using a SYBR green based quantitative PCR (qPCR) as described previously (Starnawski et al., 2017) using the primers pair Bac908F/Bac1075R (Ohkuma and Kudo, 1998).  The community bacterial 16S rRNA genes were amplified and sequenced using the Illumina MiSeq platform with a paired-end 300-bp MiSeq v3 reagent kit following procedures described by Vergeynst et al. (2019) yielding 10000-50000 reads per samples.