Changes in the prokaryotic communities occurring along a two-stage anaerobic digestion system treating the organic fraction of solid waste

•Bacterial communities with AD specialized capabilities were stable over time.•Bioreactor's vertical stratification affects the bacterial community structure.•Bacterial communities were more diverse in the second stage than in the first.•Prevotellaceae family was dominant in the hydrolytic-acidogenic stage.•Methanosaeta and Methanobacterium were dominant archaea in the second stage. Two-stage anaerobic digestion is useful for recycling of the organic fraction of municipal solid waste and wastewater; the prokaryotic communities involved in this process were characterized using massive sequencing of 16S rRNA gene amplicons. During the 60-day study the prokaryotic communities were stable in time but were affected by their position in the system. The first stage of solid waste digestion was operated in an anaerobic-hydrolytic leach bead reactor with high organic solids content, the microbial communities were dominated by members of the orders Bacteroidales (62%), Selenomonadales (15%), Lactobacillales (13%), Clostridiales (4%) and Rhodospirillales (1%). At this stage, a vertical stratification acted as a transition zone from aerobic to anaerobic environments modifying significantly the composition and structure of bacterial communities. The second stage occurred in an up-flow anaerobic sludge bed reactor specialized in acidogenesis-methanogenesis, where the leachate of the first stage was co-fed with municipal wastewater. In this stage, the bacterial community was dominated by members of the orders Pseudomonadales, Clostridiales, Burkholderiales, Bacteroidales and Syntrophobacterales (accounting for 52%), while the most abundant orders of the archaeal community corresponded to Methanosarcinales (72%) and Methanobacteriales (13%), both of them with methanogenic capacity. [Display omitted]