Highly Cited Researcher 2022

Klaus Schlaeppi: “Honored to be named a #HighlyCited2022 researcher by @ClarivateAG. Many thanks and credits to my great team @unibas_en, collaborators and colleagues!” mehr


Group outing Wasserfallen

On the 23th of August, our group exchanged their desks and lab benches for the great outdoors. We took the cable car from Reigoldswil up to Wasserfallen. Up there we did a hike with a lovely view of the Alps, followed by lunch and a short break before heading down again. At the end, the brave ones did a downhill “scooter” ride back to Reigoldswil. We also had the chance to get to know each other and the new team members better. We’re already looking forward to our next group adventure, and hopefully many new faces joining us!
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We are hiring

We are hiring!


The Plant Microbe Interactions group at the University of Basel is currently seeking talented people to join the team.

See link box


Congratulations Lisa

The ISME is the biggest conference in microbial ecology. This year it took place in Lausanne. Out of 1700 presented posters, the poster presented by Lisa Thönen won a student poster award. It shows that maize root bacteria metabolize host secondary metabolites. As a product, they form a red coloured degradation product. In her PhD, Lisa investigates where, how and why bacteria evolved this trait.


Congratulations Vero

Our PhD student Veronica Caggìa (no 6) won the World Championship of Indiaca with the Swiss women's team in Luxemburg.


Welcome Pascale

Pascale Flury joins the plant microbe interaction group as research associate. During her PhD and postdoc she worked on the genomics and the ecology of interactions of plant-beneficial Pseudomonas bacteria with pest insects with Profs. Monika Maurhofer (ETH Zurich) and Christoph Keel (University of Lausanne). She enriches the group with expertise related to #plant pathology, #biological control, #molecular diagnostics, #soil-borne plant diseases and #microbiology of compost.


mifeePs - decoding microbiota feedbacks on plants

How to decode this wonderful letter head?

Horizon Europe (HORIZON) Call: ERC-2021-COG
= This is communication relates to the Horizon Europe call for Consolidator Grants of the European Research Council from the year 2021

Project: 101044525 — mifeePs
= This is communication refers to the project mifeePs (which has the given project number)
PS: mifeePs stands for decoding microbiota feedbacks on plants and present the project submitted by Klaus Schlaeppi to the ERC COG call in 2021

GAP invitation letter (from reserve list)
= GAP stands for grant preparation; An ‘invitation for grant preparation’ simply means that the project was selected for funding; a COG project is worth 2M € - Rock n’roll!
= reserve list means that the project mifeePs - although favorably evaluated - it’s ranking was initially not high enough given the budget limit of the call. It now has moved from the reserve to the main list because higher ranked proposals dropped out or additional funding became available. Rock n’roll!


Highly Cited Researcher 2021

Each year, Clarivate™ identifies the world’s most influential researchers ─ they select few who have been most frequently cited by their peers over the last decade. In 2021, fewer than 6,700, or about 0.1%, of the world's researchers, in 21 research fields and across multiple fields, have earned this exclusive distinction.

Klaus Schläppi is among this elite group recognized for his exceptional research influence, demonstrated by the production of multiple highly-cited papers that rank in the top 1% by citations for field and year in the Web of Science™.


Block Course 'Plant Biology' 2021

The motivated and interested undergraduate students perform exciting experiments and learn about the fascinating field of 'Molecular Plant Microbe Interactions’. For the first time this part of the block course takes place at the new Biocentrum.
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Group outing Gorges de l’Areuse

On August 17th, our group exchanged their desks and their labwork for the great outdoors. We spent a GORGEous day following the wild river Areuse through all its twists and turns, eating delicious trout in the sunshine and getting to know each other better. We’re already looking forward to our next group adventure, and hopefully many new faces joining us!
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Welcome Charlotte

Charlotte Joller studied Biology at the University of Fribourg and graduated in plant and microbial sciences. She will decipher plant exudate and root microbiota dynamics during pathogen attack in a Zurich-Basel Plant Science Center – Syngenta Research Fellowship project in collaboration with Prof. Joëlle Schläpfer, University of Zürich.


Welcome Katja

Katja Stengele obtained her MSc degree from the University of Bern. She will investigate the underlying mechanisms of Arabidopsis growth feedbacks to soil microbes in her PhD.


Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field

In the work led by Selma Cadot we show that Benzoxazinoids, a class of defensive root exudate compounds, function in selectively structuring the assembly of root and rhizosphere microbiotas across different field conditions. Have a look at the video abstract. mehr


Microbiome diagnostics for sustainable agriculture

We are grateful to the Gebert Rüf Foundation for project support to work on improving field inoculation with arbuscular mycorrhizal fungi. Special thanks got to Julia Hess (Agroscope) and Dr. Natacha Bodenhausen (FiBL) driving this project with many, many helpers. Have a look at our final impact clip. mehr


Plant chemistry and food web health

Did you ever think about phytochemicals being systemically relevant? In this article, we took perspective of a food web and we highlight the role of bioactive phytochemicals in linking soils, plants, animals and humans and discuss their contributions to systems health.



New Plant Room

In our plant room at Bernoullianum we started to use the new lightchambers. We have 3 Percivals with humidity / light and temperature control and 2 Percivals with only light and temperature control. All together we have a total area of over 10m2 to grow plants under specific conditions.


Welcome Lea

New postdoc in the plant microbe interaction group! Lea Stauber has recently completed her PhD working on lifestyle evolution of Cryphonectria fungi in the group of Prof. Daniel Croll at the University of Neuchatel. Lea will work on establishing RNAseq in the group and investigating Arabidopsis’ responses to microbiota feedbacks.


Introducing our Pheno Box

The PhenoBox allows the automated quantification of 3D plant growth phenotypes in a non-invasive way. It automatically captures images of a plant from different angles and measures with an underlying image analysis algorithm over 200 phenotypic features (more details here). The PhenoBox was constructed following the publicly available construction plans and source code initially developed by Czedik‐Eysenberg et al. (2018, New Phytologist).

Thanks, Jan Wälchli! Special credits got to Daniel Lüscher and Lukas Zimmermann from our Department for their great support constructing the Phenobox!


Welcome Henry

Henry Janse van Rensburg joins the plant microbe interaction group as postdoc. He has recently finished his PhD on the interplay of metabolism and sugar signaling during biotic stress in the group of Prof. Wim Van den Ende at the Katholieke Universiteit Leuven. Henry will work on the SNF project ‘Plant Responsiveness to Microbiota Feedbacks’.


Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi

Here we describe the development of a method that measures colonization levels of plant roots by arbuscular mycorrhizal fungi using quantitative PCR. Photograph: roots colonized with arbuscular mycorrhizal fungi, stained in blue (credit: Julia Hess).”


Block Course 2020 'Plant Biology' on Instagram

In case you missed our first Instagram story. Thanks and credits to Jana Tischer and Joëlle Zweiacker, DUW.


Block Course 2020 'Plant Biology’

The motivated and interested undergraduate students perform exciting experiments and learn about the fascinating field of 'Molecular Plant Microbe Interactions’. This part of the block course takes place in the large teaching laboratory of the Biocentrum.
More pictures...

News 2

miCROPe 2019 –Emerging research priorities towards microbe-assisted crop production

In this perspective article, we carved out research priorities towards successful implementation of microbiome knowledge for modern agriculture.


Evaluation of primer pairs for microbiome profiling of diverse compartments

We evaluated the performance of commonly recommended PCR primer pairs on microbiome samples along a model food chain, including soils, maize roots, cattle rumen, and cattle and human faeces. Primer pair choice directly influenced the estimation of community changes within and across compartments and may give rise to preferential detection of specific taxa. This work demonstrates why a standardized approach is necessary to analyse microbiomes within and between source compartments along food chains.