MSc Students

Fascinated by plant microbe interactions? – Then, conduct your thesis work with us for a MSc in Plant Sciences. For more information on the degree program: MSc in Plant Sciences

Currents MSc topics

Check out the following topics to have an idea for a possible MSc thesis work. Please contact Klaus Schlaeppi for current opportunities, more information or to discuss your own idea.


Disease suppression by composts and plant-beneficial Pseudomonas

Soil-borne diseases are a major problem in agricultural production and are difficult to treat with chemical pesticides. An organic alternative is the use of compost or biocontrol microbes. However, their effectiveness is highly variable and it is not known why certain composts are able to protect plants while others are not. You will investigate what makes a compost disease suppressive.

Supervisor: Dr. Pascale Flury

MSc Maize

Benzoxazinoid metabolization by maize bacteria

Plant root exudates contain specialized metabolites that shape the root and rhizosphere microbiome. Benzoxazinoids are the main specialised metabolites of maize. Most bacteria isolated from the maize but not from the arabidopsis root environment are tolerant to antimicrobial benzoxazinoids. You investigate how bacteria cope with benzoxazinoids and potentially degrade them and how tolerance to benzoxazinoids affects colonization of the maize root and rhizosphere.

Supervisor(s): Dr. Christine Pestalozzi


Variovorax bacteria

A Variovorax strain of a 9-member synthetic community (SynCom) is able to alleviate pattern-triggered immunity fitness costs in plants. You investigate the manipulation of plant immune responses by commensal Variovorax bacteria.

Supervisor(s): Charlotte Joller, Prof. Klaus Schlaeppi


Microbiome dysbiosis

Microbiome dysbiosis

A synthetic community of 9 bacteria (SynCom 9) promotes growth in open pots at low humidity. The same SynCom 9 provokes ‘water soaked leaves’ in closed and humid conditions. You investigate what underlies such drastic phenotype switches.

Supervisor: Prof. Klaus Schläppi



Plant responsiveness to microbial feedbacks

Arabidopsis plants with different genetic backgrounds show a diverse growth responses to different microbiomes. This phenotypic diversity allows to identify regions in the plant genome that explain the differential responsiveness to microbiomes. You will study the genes that allow plants to grow better on specific microbiomes.

Supervisor(s): Dr. Henry Janse van Rensburg


Starting a MSc thesis

Step one is the identification of the thesis topic and defining your research question with your direct thesis supervisor (PhD, Postdoc, Research associate) and Klaus Schlaeppi.

You then prepare a thesis project outline consisting of a working title, an abstract, background information with references, your research question(s), the methods you will use and a timeline. You write this with input from your thesis supervisors. A thesis project outline is 1 to 2 pages A4 and sets the basis for your thesis work.

Besides having signed up for the University of Basel, you have to register for the MSc Program at the Student Office Biology. This is done by formalizing your MSc thesis with a ‘Learning Contract for Master's Thesis’ (see MSc thesis). In this form, student and supervisor(s) agree on the MSc thesis work and the learning contract is then approved by the teaching committee. Details to fill: select 50 credit points (CP), add the abstract of your project outline and specify ’see annex for details’ in 'Short description of content’ and append your thesis project outline as annex to the learning contract.

The final step is to establish a plan for your lectures. A total of 30 credit points (CP) from lectures, seminars or field trips is needed. 18 CPs come from the courses of the University (, select program structure MSc in Plant Science) and 12 CPs can be from lectures or seminars that are freely chosen. You are entitled to take classes of the Zurich-Basel Plant Sciences Center. The lecture plan is then discussed with your supervisor and recorded in a spreadsheet form (ask your supervisor). Goal is to define a program that suits your interests and future directions and also to make sure that you will have the necessary credits at the end of the MSc education.

…and coming to an end.

The MSc education concludes by submitting your MSc thesis to your direct thesis supervisor and Klaus Schlaeppi and with the MSc exam. The MSc exam is an oral examination on your specialized topic and it lasts 60 minutes (see MSc examination).

The cartoon below summarizes the administrative procedure to conclude the MSc degree in Plant Sciences. It outlines the steps and timing to finalize your MSc thesis and to register for the MSc exam at the Student Office Biology.

Completed MSc theses

MSc Loic

Leveraging soil physiochemical and microbiome variables to predict growth response of maize after inoculation with arbuscular mycorrhizal fungi

MSc Loïc Thurre

MSc monica

Understanding disease suppression by compost microbes: quantifying pathogen reduction by compost and testing Sphingopyxis spp. associated with disease suppression

MSc Mònica Camareno Rodríguez

MSc Viola

Understanding soil microbiome feedbacks on growth and defence of Arabidopsis thaliana

MSc Viola D’Adda


Exploring the role of Pseudomonas communities in the disease suppression by composts

MSc Eva Burgunder

MSc Cailtin

Tolerance and Metabolization of Host-Specific Specialized Metabolites by Maize and Arabidopsis Bacteria

MSc Caitlin Giroud

MSc Lena

Promise and predictability of a fungal inoculum for sustainable agriculture - Soil predictors for growth promotion of Cladosporium tenuissimum on Triticum aestivum

MSc Lena von Saldern
(Master in Sustainable Development)

Rain out shelter

Drought effects on arbuscular mycorrhizal fungi functioning in the context of organic and conventional farming practices

MSc Nathalie Gräppi

MSc Sam

Growth Regulating Transcription Factors and Massilia bacteria in Plant Microbiome Feedbacks

MSc Samuel Field

MSc Claudia

Microbial community dynamics and their impact on plant performance under phosphorous limiting conditions

Microbial community dynamics and their impact on plant performance under phosphorous limiting conditions

MSc Claudia Probst