The Department of Marine Microbiology and Biogeochemistry (MMB; Principal Investigator dr. Anja Spang) is looking for a highly motivated PhD student with a background in bioinformatics, phylogenetics, genomics, evolutionary biology, biochemistry or related fields who would like to contribute to a better understanding of the metabolic diversity and the deep evolutionary roots of the Archaea.

The Research

The research team of dr. Anja Spang (partially sponsored by a WISE fellowship granted by the Dutch Research Council) has a key interest in the role of evolution and symbiosis in shaping the diversity of life on Earth ranging from the origin of the archaea, the eukaryotic cell, to symbiotic relationships between different extant microbial groups, such as syntrophic and symbiotic interactions involving archaeal partners.

One research focus lies in the study of the poorly characterized enzymatic and metabolic diversity of recently discovered uncultivated archaea (including lineages belonging to the tentative deep-branching archaeal superphylum DPANN) to assess and update current hypotheses on the early evolution of metabolism along major transitions in the Tree of Life, which are based on previous limited knowledge from a limited diversity of few cultivated archaeal representatives.

The Project

Cultivating independent methods, such as metagenomics, comparative genomics, and phylogenomics, have proven to be extremely useful to reconstruct genomes of the uncultivated microbial majority and to shed light on their genomic potential and evolution. For example, such approaches have recently unveiled a large amount of uncultivated archaeal lineages profoundly expanding the known archaeal phylogenetic diversity and providing first insights into the metabolic repertoire of representatives of these lineages.

However, in-depth analyses of these genomes are required to generate reliable predictions on physiological capabilities of uncultivated archaea and to update current hypotheses on the evolution of metabolic diversity in the archaea.

In this project, we will use a combination of bioinformatics and phylogenetic approaches to analyze the diversity of the archaeal enzymatic repertoire and the evolutionary history of selected key proteins. Results will be integrated to refine hypotheses on metabolic capabilities of extant members of the archaea including their adaptations to environmental niches (e.g. specific marine ecosystems) under the influence of horizontal gene transfer. Furthermore, this data will be used to update current knowledge on the nature of the last archaeal common ancestor of Archaea. Finally, some of the predictions will be tested using microbiological and cultivation-based approaches.

We like to get in contact with a highly motivated young researcher with training in phylogenetics, phylogenomics, metagenomics, microbiology or related fields willing to learn and apply cross-disciplinary approaches.

Experience in the use of the command line and Unix, as well as in the application of programming languages such as R and Python, are of advantage. Basic knowledge of biochemistry and molecular tools is a plus. Finally, due to the international character of our research, good command of English, spoken as well as written, is a prerequisite.

Employment of this position at Royal NIOZ is by NWO (The Netherlands Organization of Scientific Research). We offer a position for 4 (fulltime) years with an excellent salary, a pension scheme, a holiday allowance of 8% of the gross annual salary, a year-end bonus, and flexible work arrangements. You may expect attractive secondary employment conditions. We offer generous relocation expenses for employees coming from abroad and support with finding accommodation.