Transcriptomic response of a continuous Nitrosomonas europaea culture to oxygen-limited growth

Nitrification is a ubiquitous, microbially mediated process in the environment and is essential in many engineered ecosystems such as aquaculture, as well as drinking water and wastewater treatment. Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The ammonia-oxidizing bacterium Nitrosomonas europaea was isolated over 100 years ago, and is the best characterized ammonia oxidizer to date. It is well documented that exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g. by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. Previous studies investigating the effect of oxygen-limited conditions on N. europaea have utilized targeted approaches to determine the transcriptional regulation of genes directly involved in nitrification and nitrifier denitrification. However, the overall transcriptional response of N. europaea to oxygen limitation remains largely unknown. Here, we combine steady-state cultivation under substrate- and oxygen-limited conditions with whole genome transcriptomics to investigate the effect of oxygen limitation on N. europaea. We observed a striking downregulation of genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the key enzyme in the CO2-fixation pathway employed by N. europaea. The downregulation of RuBisCO genes is consistent with an increased carbon fixation efficiency under low oxygen conditions. Furthermore, both heme-copper containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. The strong upregulation of the B-type heme-copper oxidase, previously proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria, was particularly striking. Based on our findings, we propose sNOR to primarily function as an alternative terminal oxidase, and not as a nitric oxide reductase. Contrary to our hypothesis, the transcription of the nitrite and nitric oxide reductase encoding genes (NirK and cNOR) known to be involved in nitrifier denitrification, did not increase significantly. Overall, our observations provide valuable insight into physiological strategies, aside from nitrifier denitrification, employed by N. europaea during oxygen-limited growth. The proposed physiological adaptations contribute to the understanding of reported high abundances of N. europaea and a wide range of other ammonia-oxidizing bacteria in transiently hypoxic or anoxic environments.