A bioreactor applied solely with ammonium and inorganic C maintains an extremely diverse archaeal and bacterial community even after nine years

The archaeal and bacterial community was determined in a continuous aerobic nitrifying reactor maintained under similar conditions for > 9 years, applied solely with ammonium as energy source and carbonate as C source. The high-throughput shotgun analysis revealed 4483 bacterial and 245 archaeal species that thrived on the metabolites provided by the autotrophic nitrifying population, mostly the ammonia oxidizing bacteria Nitrosomonas europaea and archaea Candidatus Nitrosocosmicus exaquare, and the nitrite oxidizing bacteria Nitrobacter winogradskyi and N. hamburgensis . Candidatus Nitrospira inopinata capable of oxidizing ammonia to nitrate was also detected. Although the reactor was supplied with sufficient O ₂ , the anaerobic bacteria Candidatus Kuenenia stuttgardiensis capable of oxidizing ammonium to dinitrogen gas using nitrite as the electron acceptor under anoxic conditions (anammox) and four archaeal genera of the strict Methanobacteriaceae were detected in the reactor. A wide range of genes encoding for the different processes involved in N cycling were detected including the hzo gene encoding for the hydrazine oxidoreductase participating in the anaerobic anammox process. It was found that a bioreactor applied only with ammonium as energy source and maintained for >9 years under steady state contained an extremely diverse bacterial and archaeal population and a wide range of metabolic processes related to the N and C cycle, which has not been reported before. One-Sentence Summary: Bacteria and archaea in a 9-year-old nitrifying reactor.