Integrated systems-biology platform for power-to-gas technology

Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance and gas consumption/production of three wild-type strains and one genetically engineered strain in two independent quadruplicate chemostat bioreactor experiments: 1) with molecular hydrogen and carbon dioxide; and 2) with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. We collected statistically reliable transcriptomics and proteomics data sets from these steady-state bioreactors, which we integrated within our genome-scale metabolic models. The implementation of an pan-model that contains combined reactions from all three microbes allowed us to perform an interspecies comparison of the complete omics data set. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways, such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach using fermentation and omics data with genome-scale modeling for the investigation of lesser studied metabolisms, and the biotechnological potential of Methanothermobacter spp. as production platform hosts. Individual (and comparative) gene expression analysis of RNA-seq data taken during exponential growth (bioreactors at steady state) for Methanothermobacter thermautotrophicus ΔH, Methanothermobacter thermautotrophicus Z-245, and Methanothermobacter marburgensis Marburg. Each microbe has 4 biological replicates corresponding to 4 bioreactors.