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Background  The expansion of renewable energy produced by windmills and photovoltaic panels has generated a considerable electricity surplus, which can be utilized in water electrolysis systems for hydrogen production. The resulting hydrogen can then be funneled to anaerobic digesters for biogas upgrading (biomethanation) purposes (power-to-methane) or to produce high value-added compounds such as short-chain fatty acids (power-to-chemicals).  Genome-centric metagenomics and metatranscriptomic analyses were performed to better understand the metabolic dynamics associated with H 2  injection in two different configurations of anaerobic digesters treating acidic wastes, specifically cheese manufacturing byproducts. These approaches revealed the key-genes involved in methanation and carbon fixation pathways at species level.    Results  The biogas upgrading process in the single-stage configuration increased the CH 4  content by 7%. The dominant methanogenic species responsible for the upregulation of the hydrogenotrophic pathway in this reactor was  Methanothermobacter wolfeii  UC0008. In the two-stage configuration, H 2  injection induced an upregulation of CO 2  fixation pathways producing short-chain fatty acids, mainly acetate and butyrate. In this configuration, the abundant species  Anaerobaculum hydrogeniformans  UC0046 and  Defluviitoga tunisiensis  UC0050 primarily upregulated genes related to electron transport chains, suggesting putative syntrophisms with hydrogen scavenger microbes. Interestingly,  Tepidanaerobacter acetatoxydans  UC0018 did not act as an acetate-oxidizer in either reactor configurations, and instead regulated pathways involved in acetate production and uptake. A putative syntrophic association between  Coprothermobacter proteolyticus  UC0011 and  M .  wolfeii  UC0008 was proposed in the two-stage reactor. In order to support the transcriptomic findings regarding the hydrogen utilization routes, an advanced bioconversion model was adapted for the simulation of the single- and two-stage reactor setups.    Conclusions  This is the first study investigating biogas reactor metatranscriptome dynamics following hydrogen injection for biomethanation and carbon fixation to short-chain fatty acids purposes. The same microbes showed different patterns of metabolic regulation in the two reactor configurations. It was observed an effect of the specialized acidogenic reactor on the overall microbial consortium composition and activity in the two-stage digester. There were also suggested the main species responsible for methanation, short-chain fatty acids production, and electron transport chain mechanisms, in both reactor configurations.    Electronic supplementary material  The online version of this article (10.1186/s40168-018-0583-4) contains supplementary material, which is available to authorized users.

Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics