The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

Abstract

Members of the genera <i>Proteiniphilum</i> and <i>Petrimonas</i> were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, <i>Petrimonas mucosa</i> ING2-E5A^T was isolated from a biogas reactor sample and sequenced on the PacBio <i>RSII</i> and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5A^T in close proximity to <i>Fermentimonas</i> and <i>Proteiniphilum</i> species (family Dysgonomonadaceae). ING2-E5A^T encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem <i>sus</i>CD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5A^T PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5A^T genome as a template and publicly available metagenomes of AD microbiomes revealed that <i>Petrimonas</i> species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for <i>Petrimonas</i> species. Likewise, screening of metaproteome datasets demonstrated expression of the <i>Petrimonas</i> PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of <i>Petrimonas</i> species.