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Model-based optimization of cultivation conditions for ammonia and nitrite oxidizing archaea and bacteria

 

Supervisor: Thomas Rattei

PhD student: Javier Geijo

Group: Computational Systems Biology, Centre for Microbiology and Environmental Systems Science

 

 

During the last years, the sequencing of complete genomes of nitrite oxidizing bacteria (NOB), ammonia oxidizing bacteria (AOB) and archaea (AOA) allowed to establish the first conceptual model of their metabolism. In this project we will use mathematical modeling to generate genome-wide metabolic models of NOB, AOB and AOA based on the recently obtained genome sequences. These models will be used in conjunction with comparative genomics methods to improve and enhance the genome annotations, e.g. by predicting transporters and localizing and filling holes in metabolic pathways. We will exploit these models for the optimization of cultivation conditions of NOB, AOA and AOB. Based on transcriptomic and flux data generated by other projects of this DK and retrieved from public databases, we will establish quantitative metabolic models of the pathways relevant for the N metabolism.

The project primarily involves computational work in our group and in Fabian Theis’ team, such as data processing, genome analysis as well as the generation, refinement and application of mathematical models. Mathematical predictions will be experimentally tested within the framework of this DK.

Co-Supervision: HD, AR, Secondment: Fabian Theis, Helmholtz-Center Munich, Germany

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