Two vacant PhD-positions at the University of Amsterdam in the Netherlands

The Faculty of Science occupies a leading position internationally in its fields of research and participates in a large number of cooperative programmes with universities, research institutes and businesses. The faculty has a student body of around 3,000 and 1,500 members of staff, spread over eight research institutes and a number of faculty-wide support services. A considerable part of the research is made possible by external funding from Dutch and international organisations and the private sector. The Faculty of Science offers thirteen Bachelor's degree programmes and eighteen Master’s degree programmes in the fields of the exact sciences, computer science and information studies, and life and earth sciences.

Since September 2010, the whole faculty has been housed in a brand new building at the Science Park in Amsterdam. The instalment of the faculty has made the Science Park one of the largest centres of academic research in the Netherlands.

The Institute for Biodiversity and Ecosystem Dynamics (IBED) is one of the eight research institutes of the Faculty of Science. IBED covers a wide range of subjects, in both fundamental and applied research. Our scientific studies aim at a better understanding of the dynamics of ecosystems at all relevant levels, from genes to climate change, using a truly multidisciplinary approach.

The IBED-research group Aquatic Microbiology (AMB) is led by prof. dr. Jef Huisman and consists of four senior scientific staff, three lab technicians, and a varying number of externally funded PhD students and postdocs.

Due to grants from the European Union and the University of Amsterdam, IBED has a vacancy for two PhD-students PhD student in Microbial Ecology / Microbial Systems Ecology for 38 hours/week

Vacancy number W12-171
Microbial diversity is enormous; it has been estimated that for example in the ocean more than 1.2 x 1029 microbial cells are living. However, so far only less than 1% of these cells have been isolated in pure culture. The remaining 99%, which is regarded as ‘unculturable’, represents, however, an important source for biotechnological applications. The PhD-student will participate in a European Union-funded project entitled 'Marine Microorganisms: Cultivation Methods for Improving their Biotechnological Applications’ (MACUMBA), which will develop novel
approaches and methodologies, including high-throughput procedures, for the isolation of new microorganisms from a variety of marine environments, such as marine sediments, deep-sea brines, hydrothermal vents, and the open ocean. The project will cultivate microorganisms under conditions that approach their natural environment, and will investigate the influence of cell-tocell communication on the success of isolation and growth.

Tasks
The PhD-student will contribute to different tasks in the project. He or she will isolate microorganisms from benthic marine ecosystems, such as coastal mudflats and microbial mats, by using gradient systems that mimic the conditions in the environment. Subsequently, the isolates will be characterized physiologically and their genomes will be sequenced. To improve the culture efficiency of the isolates, the PhD-student will develop so-called ‘genetic algorithms’. GA use the principle of natural evolution to solve complex optimization problems. In successive 2 iterations the GA will suggest better culture conditions, which will be tested experimentally. In addition, different approaches, such as 16S Pyrotag sequencing, metagenomics and metatranscriptomics, will be used on selected samples to determine the species composition and to get insight into specific metabolic pathways with the aim to use this information for the successful isolation of particular microorganisms (‘genome-directed isolation’).

Requirements
• Master in microbiology or microbial ecology;
• Experience with the isolation and cultivation of bacteria;
• Experience with genomic techniques;
• Experience with bioinformatics
• Ability to work in multidisciplinary research teams.

Vacancy number W12-172
In general microbial communities are diverse, consisting of many microorganisms with various interspecies interactions. Well-know interactions are competition or predation; other, less well studied, interactions are commensalism, whereby one organism benefits from another organism, and mutualism, whereby two organisms benefit from each other. All these interactions have a strong effect on the community structure and function. Within this project we will study the complex, dynamic interspecies interactions in a small, stratified lake. Sulfur bacteria play an important role in the cycling of carbon and sulfur in these lakes. Sulfide, produced by sulfate reducing bacteria in the sediment, is oxidized under oxic conditions by chemolithotrophic (‘colorless’) sulfur bacteria, and under anoxic conditions by phototrophic sulfur bacteria (purple sulfur and green sulfur bacteria). Apart from the sulfur bacteria, cyanobacteria dominate the top layers of these lakes. As these communities are exposed to diel and seasonal cycles, there are
complex, dynamic interactions between the different community members.

Tasks
The project will study competition for reduced sulfur compounds between phototrophic and chemotrophic sulfur bacteria, the facilitating and inhibiting effects of oxygen production by cyanobacteria on phototrophic and chemotrophic sulfur bacteria, and the effect of sulfide oxidation (‘detoxification’) by sulfur bacteria on cyanobacteria. For this purpose, representatives of these organisms will we grown in defined mixtures. In addition, the structure, function and dynamics of the microbial community in the stratified lake will be studied during the day and monthly using state-of-the-art meta-omic techniques. Finally, the complex interactions will be studied with in silico modeling.

Requirements
• Master in microbiology or microbial ecology;
• Experience with the isolation and cultivation of bacteria;
• Experience with genomics techniques;
• Experience with bioinformatics and mathematical modeling;
• Ability to work in multidisciplinary research teams.

More information
For additional information, please contact:
Prof. dr. Gerard Muijzer
E-mail g.muijzer@uva.nl

Appointment
The positions will begin in fall 2012. The full-time appointment will be on a temporary basis for maximum period of four years (18 months plus a further 30 months after a positive evaluation) and should lead to a dissertation (PhD thesis). An educational plan will be drafted that includes attendance of courses and (international) meetings. The PhD student is also expected to assist in teaching of undergraduates. The full-time gross monthly salary will range from € 2,042 in the first year to € 2,612 in the final year, according to the Dutch salary scales for PhD students. The Collective Labour Agreement Dutch Universities is applicable. The annual salary will be increased by 8 % holiday allowance and 8,3 % end-of-year bonus.

Job applicationApplications should include a detailed CV including a list of publications, a motivation letter, and the names and contact addresses of two references from which information about the candidate can be obtained.

Applications should be sent before September 22, 2012 to:
University of Amsterdam, Faculty of Science – dept. PZ
attn: Drs. S.H.M. Jongerius
PO Box 94216
1090 GE Amsterdam
The Netherlands

Please mark ‘strictly confidential’ and quote the vacancy number in the upper left-hand corner of the envelope. Applications can also be e-mailed to application-science(at)uva.nl.

Please quote the vacancy number in the subject field. Interviews will be held in October.

Links:
www.science.uva.nl/ibed
www.science.uva.nl/ibed-amb
www.muyzer.eu

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