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SP5 - Two PhD positions on oak ectomycorrhizal ecology and landscape genomics

PhD Researcher (m/f/d) at WSL Birmensdorf (Switzerland) - Landscape genomics of ectomycorrhizal fungi associated to oak

The Swiss Federal Institute for Forest, Snow and Landscape Research WSL is part of the ETH Domain. Approximately 600 people work on the sustainable use and protection of the environment and on the handling of natural hazards.

In the framework of the Project “PhytOakmeter” the Research Unit ‘Biodiversity and Conservation Biology’ and its ‘Ecological Genetics’ Group is searching for the duration of 4 years, with a start in summer/fall 2023 for a PhD student in “Landscape genomics of ectomycorrhizal fungi associated to oak” (f/m/d)

Project description

“PhytOakmeter” is a project funded by the German Research Foundation and the Swiss National Science Foundation revolving around acclimatization and adaptation of pedunculate oak. It explores a common oak clone from a holobiont perspective by 24 scientists from Germany and Switzerland. Symbiotic interactions with holobiont partners, including ectomycorrhizal fungi, can support host acclimation to changing conditions, with benefits for longlived trees facing climate change. However, there are serious gaps in our understanding of the ecological roles of ectomycorrhizal fungi at the level of inter- and intraspecific diversity: how do they mediate root functions and support tree adaptation and acclimation, and are ectomycorrhizal fungi adapted to their local environmental conditions?

Based on sampling sites distributed along a European transect, you will investigate signatures of local adaptation in the highly abundant ectomycorrhizal fungus Cenococcumgeophilum and how natural populations are adapted to dry conditions. You will study the effects of different C. geophilum genotypes on the symbiotic interactions with oak plants under changing biotic and abiotic environmental conditions using Ecotron, growth chamber and field experiments. Furthermore, you will explore gene expression patterns of selected C. geophilum genotypes to stressful environments using the Ecotron experiment. By integrating the results obtained and cross-examining them with those of other working groups in the Research Unit, the project aims to provide valuable information on the role of the ectomycorrhizal symbiosis on oak holobiont acclimation as well as the adaptive capacity of ectomycorrhizal fungi.

Your profile

The successful candidate holds a master’s degree in biology or environmental sciences with a strong background in microbiology, population genetics, soil ecology and/or plant-fungi interactions. You should be keen on combining field observations with controlled experiments to perform integrative data analyses including next-generation sequencing data. The “PhytOakmeter“ project offers a unique opportunity to join forces with scientists from different backgrounds and to work on the same experimental oak system. Consequently, it is essential that you have strong skills in interacting with scientists in an interdisciplinary team, spread over several institutions. In addition, we expect experience in bioinformatics, Unix and R programming, a good knowledge of English, and the ambition to communicate results in scientific papers and at conferences. Experience with geographic information system and spatial analyses would be an advantage. Conceptual and creative skills, an independent and structured way of working and a high level of motivation and team spirit complete your profile.

How to apply

Please send your complete application to Michèle Bucher, Human Resources WSL, by uploading the requested documents through our webpage. Applications via email will not be considered. The position remains open until filled. Benjamin Dauphin, benjamin.dauphin(at) and Martina Peter, martina.peter(at) will be happy to answer any questions or provide further information. The WSL strives to increase the proportion of women in its employment, which is why qualified women are particularly called upon to apply for this position.

Apply now

PhD Researcher (m/f/d) at UFZ Halle (Germany) - Adaptation and acclimation of the clonal oak’s ectomycorrhizal fungi to biotic and abiotic environmental factors

The Helmholtz Centre for Environmental Research (UFZ) with its 1,100 employees has gained an excellent reputation as an international competence centre for environmental sciences. We are part of the largest scientific organisation in Germany, the Helmholtz association. Our mission: Our research seeks to find a balance between social development and the long-term protection of our natural resources.

The job

Symbiotic interactions with holobiont partners that enhance nutrient and water uptake by trees, the ectomycorrhizal fungi, can support host acclimation to changing conditions, with benefits for long-lived trees facing climate change. There are serious gaps in our understanding of the ecological roles of ectomycorrhizal fungi at the level of inter- and intraspecific diversity: how do they mediate root functions and support tree adaptation and acclimation? Furthermore, are ectomycorrhizal fungi adapted to their local environmental conditions? The project aims to fill this knowledge gap by investigating the contribution of ectomycorrhizal symbiosis to the acclimation of oak holobiont under biotic and abiotic stressors, taking into account the endogenous rhythmic growth. The ectomycorrhizal root tip communities will be analysed in field-monitoring sites, Tree Canopy Exposition and Ecotron Experiments of the Research Unit 5571 “PhytOakmeter”. These ecological gradients and experiments will represent a wide range of environments and controlled stress situations, and will allow analysis of the modulating influence of the endogenous rhythmic growth on ectomycorrhiza formation and function. A combination of morphotyping, enzyme activity, metabarcoding and gene expression analyses supports the project's objectives. The Research Unit ( is funded by the German Research Foundation (DFG).

Your tasks

  • Contribution to joint samplings in the three platforms of the Research Unit
  • DNA, RNA and enzyme extractions of oak ectomycorrhizas and roots
  • Accessing fungal and bacterial communities by amplicon, and fungal and plant gene expression by RNA sequencing
  • Bioinformatical and statistical downstream processing of the sequencing data
  • Presenting and publishing of results on international conferences and in peer-reviewed journals
  • PhD thesis

We offer

  • Excellent technical facilities which are without parallel
  • The freedom you need to bridge the difficult gap between basic research and close to being ready for application
  • Work in inter-disciplinary, multinational teams
  • Excellent links with national and international research networks
  • Excellent support and optimal subject-specific and general training with our HIGRADE graduate school
  • Place of work Halle (Saale)
  • Contract limitations 4 years
  • Salary Remuneration according to the TVöD public-sector up to pay grade 13 including attractive public-sector social security benefits.

Your profile

  • A scientific University degree (Diploma/ M.Sc.) in biology, microbiology, ecology, bioinformatics, or related fields of science
  • Highly motivated and team-oriented
  • Broad interest in plant-associated microbial communities
  • Good statistical (preferable with R) and analysis skills
  • Very good oral and written communication skills in English
  • Travel availability
  • Driving licence B

How to apply

For more information

Apply now


Mika Tarkka (Tel. 0345 558 5221)

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