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Post-genomic characterization of Nitrospina, a major marine nitrite oxidizer


Supervisor: Holger Daims

PhD student: Anna Mueller

Group: Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science



Nitrification is a key step of the biogeochemical nitrogen cycle, but most of the organisms catalyzing this important process still are poorly characterized. Recently, our research group made significant progress by revealing unexpected features of nitrite-oxidizing bacteria that catalyze the second nitrification step (nitrite oxidation to nitrate). However, major knowledge gaps still exist regarding the biology of nitrite oxidizers. Especially little is known about marine nitrite oxidizers, although their metabolic end product nitrate is the most predominant form of fixed nitrogen in the world's oceans.

Recently we sequenced the genome of Nitrospina gracilis, which represents the most important group of marine nitrite oxidizers, and we obtained previously unmatched insights into the metabolic potential of this organism. In this project, we will further characterize Nitrospina in physiological experiments targeted to test genome-based hypotheses. Pure cultures of N. gracilis will be incubated with isotope-labelled organic carbon sources, whose uptake will be monitored by cutting-edge, single-cell chemical imaging techniques to probe the mixotrophic potential of Nitrospina. The transcriptome will be analysed after exposure of N. gracilis to different environmental conditions and potential sources of energy, nitrogen, and carbon. A main goal is to identify and confirm genes likely involved in stress response and energy-generating metabolic pathways different from aerobic nitrite oxidation. The results will be compared to experiments with yet uncultured Nitrospina spp. in freshly taken seawater and marine sediment samples. The project will yield novel insights into the functions of Nitrospina in marine ecosystems. It will involve small- and large-scale cultivation of Nitrospina, RNA-Seq-based transcriptomics, bulk nitrite oxidation rate measurements and headspace gas analyses (e.g. for NO, N2O), and single-cell physiological analyses by FISH-microautoradiography, Raman microspectroscopy, and NanoSIMS.

The project will primarily be based at the University of Vienna, and the experiments with fresh marine samples will be conducted during an extended research stay in the lab of Prof. Andreas Schramm, University of Aarhus, Denmark.


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