16S rRNA sequencing of SOB and SRB communities in the linear flow channel reactors
Partial 16S rRNA gene sequences were analysed using the bioinformatics pipeline of Quantitative Insights into Microbial Ecology (QIIME) software (www.microbio.me/qiime) as described by Caporaso et al. (2010). Fast length Adjustment of Short reads (FLASH; version 1.2.11) was used to merge paired-end reads (Mago and Salzberg, 2011). The raw sequence read trimming and filtering as well as operational taxonomic unit (OTU) picking was performed by CD-HIT-OUT at a difference distance cut-off of 0.03 (97% ID similarity at species level) (Li et al., 2012). Lastly, taxonomic assignment of OTUs was performed using the RDP 16S rRNA classifier algorithm, UCLUST (Edgar, 2010).