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Gene expression patterns of the ammonia oxidizing archaeon Nitrosophaera viennensis under changing growth conditions


Supervisor: Christa Schleper

PhD student: Logan Hodgskiss

Group: Archaea Ecology and Evolution, Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology








Ammonia oxidizing archaea are ubiquitous and abundant in terrestrial environments and probably contribute considerably to nitrification in soils. However, little is known about their central energy and carbon metabolism and their responses to environmental changes. The first and only available organism from soil that can be grown in pure culture is Nitrososphaera viennensis that was isolated by us in the departmental garden in Vienna. We have shown earlier that the metabolism of the organism differs clearly from that of AOB (ammonia oxidizing bacteria) in several aspects: For example, growth is strongly dependent on the addition of small amounts of certain organic compounds (pyruvate, oxalacetate, glyoxylate) and N2O is produced under aerobic conditions but its emission does not increase under oxygen limitation. The optimal growth of N. viennensis in the laboratory at 42°C is unexpectedly high, given the mostly lower in situ temperatures in its natural environment. In order to better understand the metabolic versatility, the ecophysiology and the adaptations and stress reactions of the organism, growth of N. viennensis on differenct carbon sources and at different temperatures will be explored and gene expression patterns will be analysed by transcriptomics. In addition, metabolomic studies with labelled substrates will be used to explore the role of organic uptake in the central metabolism. Through these studies we attempt to get deeper insights into the metabolic flexibility of the organism, its major metabolic pathways, its mixotrophy and its reactions to changing environmental conditions. The project will involve cultivation of the organism in chemostat culture fermentation under various conditions, RNA isolation for a differential RNA-Seq project (HiSeq Illumina sequencing) in time series experiments, metabolomics (in collaboration with WWe) and bioinformatic analysis of the datasets.

Co-Supervision: WWe, GJH, Secondment: Prof. Dr. Thomas Nägele, Ludwig-Maximilians University Munich.

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