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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







Exploring the Physiology of an Ammonia Oxidizing Archaeon, Nitrososphaera viennensis

The primary goal of this project is to investigate the carbon and energy metabolism of the recently isolated Nitrososphaera viennensis, an ammonia oxidizing archaeon found in soil.    At the beginning of the project, the possibility of N. viennensis growing mixotrophically was of particular interest.  However, this notion was discredited with the publication of a separate group showing the organism to be strictly autotrophic.  This revelation allowed for the reevaluation of the project.  Based on this new information, we were able to create a thermodyanic model and redesign experiments that focused on the interplay of nitrogen and carbon metabolism within the cell. Technical methods for these experiments were largely supported bythe group of Dr. Simon Rittman within the Division of Archaea Biology and Ecogenomics and Barbara Bayer (now Dr.), an associated student within the DK+ program from the Marine Biology Department. In conjunction with Prof. Dr. Wolfram Weckworth and Assoc-Prof. Dr. Stefanie Wienkoop, from the Division of Molecular Systems Biology, and Prof. Dr. Thomas Nägele, from LMU-Munich, we were able to utilize analysis techniques that integrated the simultaneous analysis of the metabolome and the proteome of N. viennensis under carbon limiation.  To our knowledge, this approach has not been utilized within the nitrogen cycling community.  As a result of these combined efforts, we were able to identify clear patterns of stress and focus on pathways within the cell that we had previously overlooked.

One of the orginally proposed methods within this project included the use of transcriptomics to evaluate the response of N. viennensis to stress.  This approach has proved useful on a collaborative project with Dr. Carolina Reyes and Prof. Dr. Stephan M. Krämer from the Environmental Geosciences Department at the University of Vienna. Combining their knowledge of the behavior of metals in the environment with our biological expertise, we successfully grew N. viennensis under copper limited conditions and identified strong transcriptional repsonses.  This is fundamental to our understanding of the energy metabolim of N. viennensis, which relies heavily on copper containing enzymes.

In addition to probling physiological questions using omic techniques, we have taken a direct approach to understanding the cell's energy metabolism.  Although fundamental to the nitrogen cycle, the complete energy pathway of N. viennesis is unknown.  To address this and other questions, we successfully attempted to obtain Blue Native protein gels of membrane proteins from N. viennensis.  Although ongoing, the preliminary results have given new evidence for the makeup of the AMO complex.  These efforts have also been supported through a collaboration with Dr. Kyle Lancaster,  an associate professor at the Department of Chemistry and Chemical Biology at Cornell University.  This collaboration was made possible through attendace of the 5th International Conference on Nitrification (ICON5).  Attendence of this and other conferences, such as the 20th European Bioenergetics Conference (EBEC),  Molecular Biology of Archaea EMBO conference, and a summer school entitled “Chemistry of Metals in Biological Systems”, have been critical in the design of experiments and success of many of the projects supported by my particular project within the DK+ program. 

Co-Supervision: Wolfgang Weckwerth, Gerhard Herndl, Secondment: Prof. Dr. Thomas Nägele, Ludwig-Maximilians University Munich.


Please find a list of publications here.

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