Process stability in anaerobic Digestion: Unveiling microbial signatures of full-scale reactor performance

Anaerobic digestion is responding to the growing demand for sustainability by exploring alternatives for methane production through renewable processes. The target is to implement stable production systems at industrial scale that can accommodate heterogeneous feedstocks with seasonal or intermittent availability. In this study, we investigated the microbiomes of six full-scale biogas plant digesters, operated under continuous production with distinct feedstock and varying operating parameters, by monitoring multiple time points over an 18-month period. This time-course experiment analyzed 114 Metagenome-Assembled Genomes alongside physico-chemical assessments to identify common and plant-specific indicators for operational management. Results identify a Limnochordia and a Dysgonomonadaceae bacteria, as well as Candidatus Methanoculleus thermohydrogenotrophicum, as widespread and potentially desirable components of the microbiota for resilient digestion of varying waste, including the peculiar olive pomace. The abundance of individual taxonomic groups and their reconstructed metabolic pathways aligned with the availability of their fermentation substrates, finding a prevalence of beta-oxidizing bacteria with lipid-rich olive pomace. Monitoring through perturbation events revealed possible causative and remediative microbiological factors, in particular Methanosarcina flavescens and Candidatus Syntrophosphaera thermopropionivorans could contribute to restoration of reactor performance. This work showcases relationships between digester operation and its microbiome, supporting microbial monitoring as a tool to increase biogas production efficiency.