Mixed method metagenome of a full-scale biogas facility collected over 19 months. bioreactor metagenome

The Surrey Biofuel Facility (SBF) is a closed-loop organic waste facility located in Surrey, British Columbia that treats organic waste originating from local households, industries, and commercial operations. The SBF operates as a dry AD process, in which the incoming waste is shredded, piled into large anaerobic tunnels, and sprayed with a concentrated liquid solution of microbes called digestate. Digestion occurs in the tunnels at 37 degrees centigrade over the course of approximately 30 days, and the liquid released by the digesting waste pile is collected and pumped to a continuously stirred tank reactor (CSTR) for re-application as digestate to later batches. At various time points over the course of 19 months, liquid digestate from the CSTR at SBF was collected for DNA sequencing. Three samples were used to generate long-read sequences on a PacBio Sequel II. Eight samples were used to generate short-read sequences on an Illumina NovaSeq S4.The three HiFi long-read samples were co-assembled and binned using the mmlong2-lite v1.0.2 pipeline which using Flye v2.9.2 in metagenome mode for assembly and MetaBAT2 v2.15, SemiBin v1.5, and GraphMB v0.1.5 for binning. Reads from each short-read Illumina sequencing sample were assembled independently using metaSPAdes v3.15.2 and binning was performed for each assembly using MetaBAT2 v2.15.Genome bins from the HiFi co-assembly and each of the eight Illumina assemblies were then clustered by nucleotide similarity using dRep v3.4.2 using an ANI threshold of 98%. The best bin from each of the resulting secondary clusters was selected using a conditional scoring algorithm that considered completeness, contamination, genome length, and presence of 16S and 23S rRNA genes.