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

Abstract

BackgroundMicroorganisms 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. ResultsHere, 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 dynamics for microbes involved in different steps of the food chain. ConclusionsThe 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. BackgroundAnaerobic environments are ubiquitous in the biosphere. Some examples are the digestive tract of animals, paddy fields, wetlands and aquatic sediments. These environments play crucial roles in the degradation of organic matter and in the global carbon cycle. The anaerobic digestion (AD) process has great societal importance since it reduces our dependence on fossil fuels via its ability to generate methane within engineered bioreactors [1]. For these reasons, the AD process has been 4 widely established as an efficient metabolic route allowing the conversion of organic wastes, agricultural residues and renewable primary products into energy and other valuable products, and accordingly has been promoted as a sustainable solution for resource recovery and renewable energy production underpinning the circular economy concept.Methane is one of the most relevant end-products generated during the methanogenesis step of the AD process, and is produced by methanogenic Archaea [2,3]. Methane production has been directly linked to the composition of the AD microbiome [4][5][6], and it is also under the control of microbial metabolism, which is in turn thermodynamically dependent on environmental parameters of the reactor [7]. The intimate connection between these parameters offers unique opportunities to improve process efficiency, which can be achieved through microbial selection or manipulation.To improve the understanding of highly diverse and interconnected networks o...

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