Abstract
The safe planetary boundary for the nitrogen cycle has been greatly exceeded. Vast increases in nitrogen input via fertilization have resulted in severe environmental consequences, causing eutrophication, biodiversity loss and public health problems. Besides agriculture, wastewater is a huge source of nitrogen pollution. In these settings, nitrification, the step-wise oxidation of ammonia via nitrite to nitrate, has a fundamental role in nitrogen mobilization and removal. Nitrification was believed to be catalyzed by distinct groups of microorganisms, the ammonia-oxidizing prokaryotes (AOP) and nitrite-oxidizing bacteria. However, our recent findings demonstrate that Nitrospira species can catalyze complete nitrification, highlighting our incomplete understanding of this important biogeochemical process. With this proposal I aim to elucidate the genomic versatility and ecophysiology of comammox (‘complete ammonia oxidation’) Nitrospira, and investigate their competition and interaction with other key nitrogen-cycling microorganisms. Ultimately, the compiled knowledge will be used to provide the basis for applying comammox bacteria to more sustainable wastewater treatment. We have developed a novel protocol, which enables us to fluorescently label the key enzyme in AOP - the ammonia monooxygenase (AMO) - in vivo. Here, we will use this method to sort and enrich AMO-containing cells for downstream targeted metagenomic analysis and pure culture isolation of novel comammox Nitrospira, complemented by enrichment approaches in dedicated bioreactors. The obtained cultures will be used to investigate their ammonia and oxygen affinities, the key parameters presumably distinguishing comammox Nitrospira from canonical AOP, and to probe them for novel physiologies, including nitrite comproportionation. Subsequently, we will apply these parameters to investigate under which culture conditions comammox Nitrospira can outcompete other nitrifiers, and when they maximize nitrite production for efficient interaction with anaerobic ammonium-oxidizing (anammox) bacteria. Lastly, we will translate the assembled knowledge into design principles that apply comammox in an optimized partial nitritation/anammox system with improved stability and energy efficiency.
Netherlands