Ecological Processes Affecting Long-Term Eukaryote and Prokaryote Biofilm Persistence in Nitrogen Removal from Sewage

The factors affecting long-term biofilm stability in sewage treatment remain largely unexplored. We therefore analyzed moving bed bioreactors (MBBRs) biofilm composition and function two years apart from four reactors in a nitrogen-removal sewage treatment plant. Multivariate ANOVA revealed a similar prokaryote microbiota composition on biofilm carriers from the same reactors, where reactor explained 84.6% of the variance, and year only explained 1.5%. Eukaryotes showed a less similar composition with reactor explaining 56.8% of the variance and year 9.4%. Downstream effects were also more pronounced for eukaryotes than prokaryotes. For prokaryotes, carbon source emerged as a potential factor for deterministic assembly. In the two reactors with methanol as a carbon source, the bacterial genus Methylotenera dominated, with M. versatilis as the most abundant species. M. versatilis showed large lineage diversity. The lineages mainly differed with respect to potential terminal electron acceptor usage (nitrogen oxides and oxygen). Searches in the Sequence Read Archive (SRA) database indicate a global distribution of the M. versatilis strains, with methane-containing sediments as the main habitat. Taken together, our results support long-term prokaryote biofilm persistence, while eukaryotes were less persistent.