Adaptation of a microbial community to demand-oriented biological methanation

Abstract

Background: Biological conversion of the surplus of renewable electricity and carbon dioxide (CO₂) from biogas plants to biomethane (CH₄) could support energy storage and strengthen the power grid. Biological methanation (BM) is linked closely to the activity of biogas-producing Bacteria and methanogenic Archaea. During reactor operations, the microbiome is often subject to various changes, e.g., substrate limitation or pH-shifts, whereby the microorganisms are challenged to adapt to the new conditions. In this study, various process parameters including pH value, CH₄ production rate, conversion yields and final gas composition were monitored for a hydrogenotrophic-adapted microbial community cultivated in a laboratory-scale BM reactor. To investigate the robustness of the BM process regarding power oscillations, the biogas microbiome was exposed to five hydrogen (H₂)-feeding regimes lasting several days.

Results: Applying various "on-off" H₂-feeding regimes, the CH₄ production rate recovered quickly, demonstrating a significant resilience of the microbial community. Analyses of the taxonomic composition of the microbiome revealed a high abundance of the bacterial phyla Firmicutes, Bacteroidota and Thermotogota followed by hydrogenotrophic Archaea of the phylum Methanobacteriota. Homo-acetogenic and heterotrophic fermenting Bacteria formed a complex food web with methanogens. The abundance of the methanogenic Archaea roughly doubled during discontinuous H₂-feeding, which was related mainly to an increase in acetoclastic Methanothrix species. Results also suggested that Bacteria feeding on methanogens could reduce overall CH₄ production. On the other hand, using inactive biomass as a substrate could support the growth of methanogenic Archaea. During the BM process, the additional production of H₂ by fermenting Bacteria seemed to support the maintenance of hydrogenotrophic methanogens at non-H₂-feeding phases. Besides the elusive role of Methanothrix during the H₂-feeding phases, acetate consumption and pH maintenance at the non-feeding phase can be assigned to this species.

Conclusions: Taken together, the high adaptive potential of microbial communities contributes to the robustness of BM processes during discontinuous H₂-feeding and supports the commercial use of BM processes for energy storage. Discontinuous feeding strategies could be used to enrich methanogenic Archaea during the establishment of a microbial community for BM. Both findings could contribute to design and improve BM processes from lab to pilot scale.

Keywords: Acetoclastic methanogens; Biogas upgrade; Biological methanation; Hydrogen starvation; Hydrogenotrophic methanogens; Metaproteomics; Microbial food web; Power to methane; Renewable energy.

Fig. 1

Schematics of the laboratory scale setup for the biological methanation of biogas. Hydrogen produced using a polymer electrolyte membrane (PEM) electrolyser

Fig. 2

Time course of the biological methanation process during H₂-feeding experiments. A H₂-feeding regimes and sampling time of the biological methanation reactor; the selected samples were further used for statistical analysis, B volume fraction of the product gases, C community abundance. The unclassified taxon in the community composition, refers to the sum of spectral counts assigned to the low abundant metagenome-assembled genomes (MAGs) including uncategorised MAGs (MAG1 and MAG4) and MAG12 (Lutispora) and MAG8 (Methanobacteriaceae) and also the non-binned metagenome. See details of the microbial community in Additional file 1

Fig. 3

Protein profiles of the biological methanation reactor during discontinuous H₂-feeding (A) Protein extracts (25 µg) of the third sample were loaded for sodium dodecyl sulphate–polyacrylamide gel electrophoresis. 12/12* shows the experiment with 20% of nominal H₂-feeding (BM-12/12–20%). The white dashed lines enclose areas of visible variations in protein profiles. B Principal component analysis (PCA) plot of the 1000 most abundant metaproteins based on the Euclidean similarity index. The PCA plot reflects the development of microbial communities over the experiment period. See details of PCA plot generation in Additional file 4

Fig. 4

Principal component analysis (PCA) of the biogas microbiome to identify changes in the metabolic activity for two H₂-feeding experiments (BM-24/0, filled rectangle and BM-12/12, filled circle). To avoid an overcrowded PCA plot, only the mean values of the samples of these two H₂-feeding regimes are shown. See details of PCA plot data generation in Additional file 6

Fig. 5

Differential expression of proteins in Methanothrix for BM-24/0 and BM-12/12 displayed in the Kyoto Encyclopaedia of Genes and Genomes (KEGG) map of the central carbon metabolism (map01200). Colours correspond to logarithmic expression ratio [X = Log₂ (KO _BM-12/12/KO _BM-24/0)]. p > 0.05 considered significant, p ≤ 0.05 see colour legend at the right (t test). KO (KEGG Orthology) values are the mean normalised values of the abundance of defined orthologs in the metaproteins of the BM pattern. Further details of KEGG map data generation are available in Additional file 8

Fig. 6

Relative abundance of extracellular proteolytic and hydrolytic enzymes for different samples of H₂-feeding experiments. Extracellular secretion of (A) proteases and peptidases, (B) glycoside hydrolases and glycosyltransferases during H₂-feeding experiments. The spectral counts were normalised based on the total spectral count for each sample. Further details for generation of the plots are available in Additional files 9 and 10

Fig. 7

Microbial food web of a biological methanation (BM) process considering continuous H₂-feeding (BM-24/0, blue) and discontinuous H₂-feeding (BM-12/12, orange) experiments including in-/organic substrates and intermediates. The size of the boxes represents the abundance of the microbial groups of the last sample of the aforementioned feeding regimes. The full grey arrows depict the main substrate and product of the hydrogenotrophic BM process, whereas the other type of lines (BM-24/0, blue; BM-12/12, orange) are assigned to biomass (dash–dot), monomers/intermediates (dash) and acetate (dot)