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 1635 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 dynamics for microbes involved in different steps of the food chain. 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.

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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

BackgroundThe 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 H2 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.ResultsThe biogas upgrading process in the single-stage configuration increased the CH4 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, H2 injection induced an upregulation of CO2 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.ConclusionsThis 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 materialThe online version of this article (10.1186/s40168-018-0583-4) contains supplementary material, which is available to authorized users.

29Background 30 Microorganisms in biogas reactors are essential for degradation of organic matter and methane 31 production through anaerobic digestion process. However, a comprehensive genome-centric 32 comparison, including relevant metadata for each sample, is still needed to identify the globally 33 distributed biogas community members and serve as a reliable repository. 34 Results 35Here, 134 publicly available datasets derived from different biogas reactors were used to recover 36 1,635 metagenome-assembled genomes (MAGs) representing different bacterial and archaeal 37 species. All genomes were estimated to be >50% complete and nearly half were ≥90% complete 38 with ≤5% contamination. In most samples, specialized microbial communities were established, 39 while only a few taxa were widespread among the different reactor systems. Metabolic 40 reconstruction of the MAGs enabled the prediction of functional traits related to biomass 41 degradation and methane production from waste biomass. An extensive evaluation of the replication 42 index provided an estimation of the growth rate for microbes involved in different steps of the food 43 chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other 44 underexplored taxa suggests their specific involvement in the anaerobic degradation of organic 45 matter. 46 Conclusions 47 The outcome of this study highlights a high flexibility of the biogas microbiome. The dynamic 48 composition and adaptability to the environmental conditions, including temperatures and a wide 49 range of substrates, were demonstrated. Our findings enhance the mechanistic understanding of 50 anaerobic digestion microbiome and substantially extend the existing repository of genomes. The 51 established database represents a relevant resource for future studies related to this engineered 52 ecosystem. 53 3 54Background 55 Anaerobic environments are ubiquitous in the biosphere, some examples are the digestive tract of 56 animals, paddy fields and aquatic sediments. These environments play crucial roles in the 57 degradation of organic matter and in the global carbon cycle [1,2]. The anaerobic digestion (AD) 58 process is also an example of such an environment, having great societal importance since it 59 reduces our dependence on fossil fuels via its ability to generate methane within engineered 60 bioreactors [3]. For these reasons, the AD process has been widely acknowledged as an efficient 61 biochemical route allowing the conversion of organic wastes into energy and other valuable 62 products, and has been posited as a sustainable solution for resource recovery and renewable energy 63 production underpinning the circular economy concept [4]. Apart from biowaste valorization, this 64 process is also of great importance for nutrient recycling, since it stabilizes the nitrogen compounds 65 making them more easily assimilable by plants, reducing nitrogen leakage to soil and groundwater. 66 Methane is one of the most relevant end-products generated during the meth...