New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

Abstract

Background Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository. Results Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1,635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be >50% complete and nearly half ≥90% complete with ≤5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth rate for microbes involved in different steps of the food chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other underexplored taxa suggests their specific involvement in the anaerobic degradation of organic matter. Conclusions The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem. Keywords Anaerobic digestion, Metagenome-Assembled Genomes, Biogas, Microbial community structure, Functional reconstruction

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste

“…This is in accordance with the findings that thermophilic systems harbor a lower number of species compared to mesophilic reactors [69,70]. In contrast, the degradation of complex substrates was previously linked to a high diversity whereas a smaller number of species was identified in reactors that degrade simple substrates [44]. Overall, the microbial community identified by amplicon sequencing was in good coherence with the outcomes of the metagenomic approach for PFL9 (Figs.…”

“…Defluviitoga utilize a remarkable variety of complex carbohydrates such as xylan, pullulan, lichenan, galactan, chitin and cellulose, among others [42,43] producing acetate, ethanol, hydrogen, and carbon dioxide. Defluviitoga tunisiensis was also identified as widespread and abundant suggesting a central role in thermophilic biogas reactors [44]. Among the highest number of intracellular and extracellular carbohydrateactive enzymes (CAZymes) were identified in the Defluviitoga MAG-R13, which further support their importance for the initial breakdown of macromolecular compounds (Fig.…”

“…In five reactors, Methanosarcina accounted for 0.1-0.7% of Archaea, which is equivalent to a maximum of 0.008% of the total prokaryotic iTags. This very low relative abundance is contradicting to studies that identified Methanosarcinales as abundant core members of the archaeal community in AD [4,6,7,44]. More quantitative methods such as fluorescence in situ hybridization will be necessary to estimate exact Bacteria to Archaea ratios; however, the dominance of strictly hydrogenotrophic over acetoclastic methanogens within the archaeal community points to a favorable opportunity for SAOB in these AD systems.…”

“…Phylogeny of metagenome assembled genomes based on concatenated marker protein sequences and selected metabolic functions encoded in their genomes (b). Further information about contamination and completeness of the MAGs is provided in Additional file 1: gradually more specialized community in the later steps of AD [44][45][46]. Several complete modules for amino acid metabolism and degradation were detected in the Sphingobacteriales MAG-R11 suggesting uncultured Bacteroidetes as degrader of proteinaceous material besides their capability to utilize carbohydrates ( Fig.…”

Microbiota of the Therapeutic Euganean Thermal Muds with a Focus on the Main Cyanobacteria Species

“…Properties of the final genome sequence were determined using QUAST (v5.0.2) [ 56 ]. The sequences of 16S rRNA gene were extracted from the genome using a custom perl script [ 57 ] and the similarity with the non-redundant NCBI (nrNCBI) public database was determined. All public microbial genomes belonging to the Cyanobacteria phylum have been downloaded from the NCBI database (n:1471, 10 June 2019) and a local database was established.…”