title: bioreactor sludge metagenone
design: DNA extraction from anaerobic biomass was performed with FastDNA SPIN Kit for Soil DNA Extraction (MP Biomedicals). The sequencing was performed by the company Genone (Rio de Janeiro, Brazil). The primer sets used for the 16S RNAr gene were 341F/806R (region V3V4) for Bacteria Domain and U519F/806R (region V4) for the Archaea Domain. Sequence analyses were performed using the Uparse software (Uparse v7.0.1001http://drive5.com/uparse/) (Edgar, 2013). Sequences with 97% similarity were assigned to the same operational taxonomic units (OTU). Representative sequence for each OTU was screened for further annotation. For each representative sequence, the GreenGene Database (http://greengenes.lbl.gov/cgi-bin/nph-index.cgi) (DeSantis et al., 2006) was used based on RDP3 classifier (Version 2.2, http://sourceforge.net/projects/rdp-classifier/) (Wang et al., 2007) algorithm to annotate taxonomic information. In order to study the phylogenetic relationship of different OTUs, and the difference of the dominant species in different samples (groups), multiple sequence alignments were conducted using the MUSCLE software (Version 3.8.31http://www.drive5.com/muscle/) (Edgar, 2013). All these indices were calculated using QIIME (Version 1.7.0) and displayed with R software (Version 2.15.3).