Search

Background: Carbon fixation through biological methanation has emerged as a promising technology to produce renewable energy in the context of the circular economy. The anaerobic digestion microbiome is the fundamental biological system operating biogas upgrading and is paramount in power-to-gas conversion. Carbon dioxide (CO2) methanation is frequently performed by microbiota attached to solid supports generating biofilms. Despite the apparent simplicity of the microbial community involved in biogas upgrading, the dynamics behind most of the interspecies interaction remain obscure. To understand the role of the microbial species in CO2 fixation, the biofilm generated during the biogas upgrading process has been selected as a case study. The present work investigates via genome-centric metagenomics, based on a hybrid Nanopore-Illumina approach the biofilm developed on the diffusion devices of four ex situ biogas upgrading reactors. Moreover, genome-guided metabolic reconstruction and flux balance analysis were used to propose a biological role for the dominant microbes. Results: The combined microbiome was composed of 59 species, with five being dominant (> 70% of total abundance); the metagenome-assembled genomes representing these species were refined to reach a high level of completeness. Genome-guided metabolic analysis appointed Firmicutes sp. GSMM966 as the main responsible for biofilm formation. Additionally, species interactions were investigated considering their co-occurrence in 134 samples, and in terms of metabolic exchanges through flux balance simulation in a simplified medium. Some of the most abundant species (e.g., Limnochordia sp. GSMM975) were widespread (~ 67% of tested experiments), while others (e.g., Methanothermobacter wolfeii GSMM957) had a scattered distribution. Genome-scale metabolic models of the microbial community were built with boundary conditions taken from the biochemical data and showed the presence of a flexible interaction network mainly based on hydrogen and carbon dioxide uptake and formate exchange. Conclusions: Our work investigated the interplay between five dominant species within the biofilm and showed their importance in a large spectrum of anaerobic biogas reactor samples. Flux balance analysis provided a deeper insight into the potential syntrophic interaction between species, especially Limnochordia sp. GSMM975 and Methanothermobacter wolfeii GSMM957. Finally, it suggested species interactions to be based on formate and amino acids exchanges. AQaLxbUWFz91qWxiAB1_X5 Video Abstract [ABSTRACT FROM AUTHOR]

Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the Earth's climate. These ecological niches are characterised by low free oxygen and oxidants, or lack thereof. Under these conditions, interactions between species are essential for supporting the growth of syntrophic species and maintaining thermodynamic feasibility of anaerobic fermentation. Kinetic models provide a simplified view of complex metabolic networks, while genome-scale metabolic models and flux-balance analysis (FBA) aim to unravel these systems as a whole. The target of this review is to outline the main similarities, differences and challenges associated with kinetic and metabolic modelling, and describe state-of-the-art modelling practices for studying syntrophies in the anaerobic digestion (AD) case study. [Display omitted] • Anaerobic microbes play a significant role in the global biogeochemical cycle. • Mathematical models explain anaerobic processes, including bioconversion abilities, growth requirements and inhibitor susceptibility. • Kinetic modelling and FBA, are outlined, highlighting strengths and limitations. • The AD system is used as case of study to discuss modelling of syntrophies. [ABSTRACT FROM AUTHOR]

Anaerobic digestion is a key biological process for renewable energy, yet the mechanistic knowledge on its hidden microbial dynamics is still limited. The present work charted the interaction network in the anaerobic digestion microbiome via the full characterization of pairwise interactions and the associated metabolite exchanges. To this goal, a novel collection of 836 genome-scale metabolic models was built to represent the functional capabilities of bacteria and archaea species derived from genome-centric metagenomics. Dominant microbes were shown to prefer mutualistic, parasitic and commensalistic interactions over neutralism, amensalism and competition, and are more likely to behave as metabolite importers and profiteers of the coexistence. Additionally, external hydrogen injection positively influences microbiome dynamics by promoting commensalism over amensalism. Finally, exchanges of glucogenic amino acids were shown to overcome auxotrophies caused by an incomplete tricarboxylic acid cycle. Our novel strategy predicted the most favourable growth conditions for the microbes, overall suggesting strategies to increasing the biogas production efficiency. In principle, this approach could also be applied to microbial populations of biomedical importance, such as the gut microbiome, to allow a broad inspection of the microbial interplays. Image 1 • Inspection of interactions among 836 microbial species with flux balance analysis. • Dominant microbes are often profiteers in the interaction. • Interactions based on amino acid exchanges are crucial for solving auxotrophies. • Positive interplays are more likely to occur interphylum than intraphylum. • External hydrogen supply decreases the rate of negative co-growth. [ABSTRACT FROM AUTHOR]