Fig. 4

Bacterial (phylum level and top 50 OTUs level) and archaeal (genus level) structure dynamics over time as assessed by high-throughput 16S rRNA amplicon sequencing for: a–c the LNR reference reactor, d–f the free ammonia intoxicated reactor, HNR1, g–i HNR2 and j–l HNR3. The data presented correspond to slurry samples collected on Mondays. “Process reconditioning I, II, III”, “Process recovery” and “Process stability test” refer to the stages and phases described in Table 1. We refer to the Additional file 1: Table S1 for the taxonomic affiliation of the bacterial OTUs