Anaerobic digestion, a virtuous process to reduce and reuse biowaste to obtain renewable bioenergy, is often dramatically subject to process failure during long timescale operation. This study aimed to evaluate the process robustness and reliability by elucidating the composition of microbial populations and the link with process parameters under a wide range of different operating conditions in long-term semicontinuous reactors. Mesophilic semipilot digesters were fed with real urban biowaste, namely, food waste alone or food waste with activated sludge, to explore the impact of feedstock composition and organic loading rate (OLR: 0.8–3.5 kgVSfed m−3d−1) on volatile fatty acid (VFA) composition and pattern, biomethane production, and core microbiome dynamics. The major bacterial phyla were Bacteroidetes (basically more abundant when the feedstock was only food waste), followed by Chloroflexi and Firmicutes, while Euryarcheota hydrogenotrophic methanogens, mainly represented by members of the Methanomicrobiales family, prevailed in all systems. During monodigestion of food waste, however, independent of the OLR, methanogenic conversion of fermentative end-products decreased progressively after 1 HRT. In particular, the observed propionate and butyrate accumulations seemed to derive from thermodynamic limitations due to the increase in hydrogen levels, indicative of progressively lower H2 consumption rates. However, the induced process recovery assured a large degradation of fatty acids with higher carbon chain lengths together with methane production, suggesting the upswing of hydrogenotrophic methanogen activity emerging after stressful conditions. The addition of a minimal amount of sludge boosted the methane production rates (up to 0.29 ± 0.1 Nm3CH4 kg−1VSfed) along with excellent process stability, also at a high OLR, creating a robust methanogen community shaped by high biodiversity. Methanospirillum and Candidatus Methanofastidiosum, strictly related to the codigestion systems, have a large H2 consumption capacity, thus preventing thermodynamic bottlenecks and process failure.
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