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

Irena Maus,Daniel Wibberg,Dirk Benndorf,Robert Heyer,Alexander Sczyrba,Michael Klocke,Geizecler Tomazetto,Alfred Pühler,Liren Huang,Andreas Schlüter,Boyke Bunk,Julia Hassa,Tom Tubbesing,Vladimir Zverlov,Cathrin Spröer

doi:10.3390/microorganisms8122024

Abstract

Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-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-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas 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 Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.

Highlights

Anaerobic digestion (AD) is commonly applied for treatment of organic wastes in order to achieve reduction of waste combined with parallel recovery of bioenergy [1,2]
General features of the P. mucosa ING2-E5AT genome are summarized in Table 1 and Figure 1
Analysis of the P. mucosa ING2-E5AT genome for the presence of horizontally acquired DNA elements resulted in the identification of 27 genomic islands (Figure 1) and putative phage genes

Summary

Introduction

Anaerobic digestion (AD) is commonly applied for treatment of organic wastes in order to achieve reduction of waste combined with parallel recovery of bioenergy [1,2]. The degradation of organic matter is a complex microbial process featuring interaction of several groups of microorganisms with different interacting or even interfering metabolic capabilities and growth requirements [3]. Several factors causing process inhibition have been identified, such as temperature fluctuations, foaming, high concentrations in hydrogen sulfide or ammonia [4,5,6,7], imbalanced levels of light or heavy metals, the presence of interfering organic substances such as halogenated alkanes or aromatic compounds [8] as well as increased organic loading rates (OLR) [9,10]. The most frequent incident type described in literature resulting in process inhibition is the accumulation of ammonia [3]. Due to inhibition of syntrophic volatile fatty acid (VFA) oxidizers, high ammonia concentrations result in VFA accumulation which subsequently inhibits methanogenesis. Ammonia directly inhibits methanogens [11]

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