Speaker:

Dr. Sebastian Lücker Department of Microbiology, Radboud University, Nijmegen, the Netherlands

Abstract:

Nitrification is a two-step process that was assumed to be catalyzed by distinct functional groups of microorganisms. The recent discovery of complete nitrifiers within the genus Nitrospira overturned this belief and indicated our still incomplete understanding of the diversity of ammonia-oxidizing microorganisms. Furthermore, these so-called comammox bacteria are closely related to nitrite-oxidizing Nitrospira, which are impossible to distinguish using 16S rRNA-based methods. Therefore, we developed a novel activitybased protein profiling protocol that allows the in situ detection of ammonia-oxidizing bacteria via fluorescence microscopy. In combination with 16S rRNA-targeted fluorescence in situ hybridization, this protocol enables the detection and phylogenetic identification of ammonia monooxygenase containing cells, directly linking function to identity. Finally, we combined this protocol with fluorescence-activated cell sorting and metagenomic sequencing, resulting in the targeted retrieval of novel betaproteobacterial ammonia oxidizer and comammox Nitrospira genomes. Furthermore, we investigate interactions between comammoxand anaerobic ammoniumoxidising (anammox) bacteria. Therefore, we inoculated a bioreactor with biomass from a culture highly enriched in these N-cycling bacteria. Activity assays using labelled ammonia under oxygen-limited conditions showed the production of double labelled dinitrogen gas, indicating that comammox Nitrospira in this culture perform partial ammonia oxidation to nitrite, which is subsequently used by anammox. Intriguingly, the culture showed increased activity upon addition of nitrate, suggesting that comammoxNitrospiracan couple ammonia oxidation to nitrate reduction, thus performing nitrite comproportionation. Since the produced nitrite will serve as co-substrate for anammox, these results demonstrate that comammoxand anammoxbacteria can be grown as co-operators rather than competitors.