Analysis of volatile fatty acid degrading microbial communities producing biogas using Illumina and Oxford Nanopore metagenome sequencing approaches

We studied the effect of different feeding regimes and organic loading rates in context of anaerobic digestion. By feeding only acetate, propionate and butyrate to the biogas reactors the anaerobic digestion process was reduced to acetogenesis and methanogenesis. The microbial community was analyzed by a metagenome sequencing approach combining short-read (Illumina MiSeq) and long-read (Oxford Nanopore) sequencing techniques. Methanothrix dominated the whole community but was strongly reduced in abundance at higher organic loading rates. The bacterial community composition differed strongly between reactors. In contrast, the functional potential was similar in all reactors. Based on the functional annotation of predicted genes, representative genes of pathways of interest were examined. Among the bacterial genera, Desulfotomaculum and Clostridium showed the genetic potential for butyrate and propionate degradation. In total, 27 hybrid metagenome-assembled genomes (MAGs) based on Illumina and Nanopore reads, were reconstructed, which represent 18 potential new species - 15 of them new bacterial species.