PhD position ‘Harnessing compost microbes for new crop protection products against foliar diseases’

Do you want to develop new sustainable plant protection products based on microorganisms and their metabolites? The University of Basel has an open position for a 4-year PhD position to work on new crop protection products.

Thesis Topic

Copper fungicides are widely used due to a lack of efficient alternatives, and need to be replaced urgently due to their unfavourable profile. There is consensus that several new sustainable alternatives need to be developed to reach the goal of organic farming without copper. In this project, they want to identify new bacterial and fungal strains with a protective effect against important foliar diseases (grapevine downy mildew caused by Plasmopara viticola and apple scab caused by Venturia inaequalis).

You will focus on strains producing antimicrobial metabolites or inducing resistance in plants and will consider the use of living strains as well as isolated metabolites. To find suitable strains, you will explore the microbiome of disease-protective compost extracts, which are known to contain a plethora of mostly unexplored microorganisms. The main research questions are:

  • Can microorganisms present in suppressive composts protect plants from foliar pathogens?
  • What is the mode of action of the beneficial microorganisms? and
  • What microbial metabolites are associated with the beneficial activity of the microorganisms?

You will use an innovative approach combining classical plant-pathogen bioassays and microbiology with modern molecular methods (HTS-based metabarcoding/biostatistics) and state-of-the-art analytical chemistry.

This 4-year PhD-Thesis-Project is based on a collaboration of the “Crop Protection and Phytopathology” group at the Research Institute of Organic Agriculture FiBL, the Plant Microbe Interactions Group at the University of Basel and the Pharmaceutical Biology Group at the University of Basel. Therefore, the PhD project will be conducted in all three research groups. Through this project, you will gain a comprehensive understanding of molecular and classic microbiology as well as analytical chemistry, from the design of pot experiments to lab work and data analyses.

Your assignments

  • Adaption and performing of plant-pathogen bioassays and in vitro tests to evaluate the efficacy of compost microorganisms/microbial consortia;
  • Taxonomic identification of microorganisms involved in plant protection using high-throughput sequencing followed by isolation techniques;
  • Bioinformatic and statistical analyses of metabarcoding data as well as adaptation and development of analytical pipelines and R-codes;
  • Identification of active compounds produced by beneficial microorganisms using, e.g., HPLC-MS and NMR spectroscopy;
  • Presentation of research findings at national and international conferences;
  • Publication of the results in scientific journals.

Your profile

  • MSc degree in plant science, microbiology, ecology, agronomy or related field with a strong interest in phytopathology, analysis of microbial communities, molecular genetics, and analytical chemistry;
  • Experience with statistics (R);
  • Achievement-oriented, open-minded personality with strong self-motivation and spirit for teamwork;
  • Flexibility to work at three different institutes;
  • A very good level of English (spoken and written), German skills are an advantage.

Application

They accept only online applications. Online applications must contain an application letter, your CV, a copy of certificates/Diplomas (MSc &BSc) and contact details of two references, to be submitted on the application portal.

Applications are welcome until the position is filled and will be reviewed starting July 29, 2024. For more information, contact Dr. Barbara Thürig (Barbara.thuerig@fibl.org), Dr. Pascale Flury (pascale.flury@unibas.ch) or Prof. Olivier Potterat (olivier.potterat@unibas.ch )