title: Cultivation day 16
design: Sequencing of DNA samples from cultivation experiments was done targeting v4 and v5 regions with the primer pair of 515F (GTGYCAGCMGCCGCGGTAA) and 926R (CCGYCAATTYMTTTRAGTTT) (Parada, Needham, & Fuhrman, 2016). Paired-end sequenced reads were assembled using PEAR v. 0.9.11 (Zhang, Kobert, Flouri, & Stamatakis, 2014) with default settings. Mothur (v. 1.40.3) was used for demultiplexing and quality control. Primer sequences were removed using Cutadapt (v. 1.16, (Martin, 2011))  and the sequences which did not contain primers were discarded. The resulting dataset was analyzed for chimeric sequences, dereplicated and clustered with Vsearch using 97% identity threshold (v2.8.0, (Rognes, Flouri, Nichols, Quince, & Mahe, 2016)). Obtained sequences were classified using Silva database, version 138 (Quast et al., 2013)  with a threshold of 97% and further processed with QIIME (v. 1.9.1, (Kuczynski et al., 2011)) .