Microbial community structure
DNA from mixed bioreactor samples were extracted using the DNeasy
UltraClean Microbial Kit (Qiagen, The Netherlands). Approximately 250 mg
wet biomass was treated according to the standard protocol except an
alternative lysis was implemented. This included a combination of 5
minutes of heat (65ºC) followed by 5 minutes of bead-beating for cell
disruption on a Mini-Beadbeater-24 (Biospec, U.S.A.). After extraction
the DNA was checked for quality by gel electrophorese and quantified
using a Qubit 4 (Thermo Fisher Scientific, U.S.A.).
After quality control, samples were sent to Novogene Ltd. (Hongkong,
China) for amplicon sequencing of the V3-4 region of the 16S-rRNA gene
(position 341-806) on an Illumina paired-end platform. After sequencing,
the raw reads were quality filtered, chimeric sequences were removed and
OTUs were generated on the base of ≥ 97% identity. Subsequently,
microbial community analysis was performed by Novogene using Mothur &
Qiime software (V1.7.0). For phylogenetical determination a most recent
SSURef database from SILVA (http://www.arb-silva.de/) was used.