PSC Grant

Syngenta-PSC Fellowship for P. Flury, G. Garland, and S. Dötterl

We are happy to announce that the project 'Biocontrol composts: Tackling soilborne plant diseases in a changing climate' has been selected for a Syngenta-PSC Fellowship. The project will be led by Pascale Flury (Unibas, PMI) together with Gina Garland and Sebastian Dötterl from ETH Zurich and will include a collaboration with the Research Institute of Organic Agriculture (FiBL). We are excited that Eva Burgunder will soon start as a PhD student on this project. She will be studying how climate change impacts the development of soilborne diseases and how a combination of compost and biocontrol agents can improve soil and plant health under different climatic conditions.

pic eva

Congratulations Eva for your MSc degree!

In her MSc thesis, Eva Burgunder studied the role of Pseudomonas communities in the disease suppression by composts. Using a recently developed amplicon sequencing method that provides unprecedented resolution within the genus Pseudomonas, she compared the Pseudomonas communities in the rhizoplane of plants grown in suppressive and non-suppressive composts. Her analysis revealed that the Pseudomonas communities derived from composts that were effective against a soilborne pathogen were distinct from those from ineffective composts.

MSc Caitlin

Congratulations Caitlin for your MSc degree!

In her MSc thesis, Caitlin Giroud studied whether root bacteria differ in their capacity to deal with host-specific plant secondary metabolites. She examined maize and Arabidopsis bacteria for their tolerance and metabolization of maize-derived benzoxazinoids and Arabidopsis-derived coumarins. The vitro experiments revealed that native bacteria tolerate the
specialized metabolites from their host plant better than non-host bacteria. This work suggests that bacterial strains adapt to the exudate compounds of their host plants.

MSc Lena

Congratulations Lena for your MSc degree!

Lena von Saldern investigated the effectivity of a fungal inoculum for its prospects seedling establishment. In her MSc work she studied the context-dependence of successful fungal inoculations. The inoculum only mildly supported wheat establishment and mostly in combination with a fertilization treatment. Lena von Saldern found a model combining biological, physical, and chemical soil parameters that explained 90% of the soil-to-soil variation in inoculation success!


Study in Nature Microbiology: Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi are known to enhance plant nutrient uptake and reduce plant stress. However, agricultural implementation suffers from unpredictable inoculation success. We have conducted large-scale field-inoculations with the goal to model the variable effects on maize yield. With few soil parameters and mainly soil fungal indicators, we could predict the inoculation effects in 9 out of 10 fields! Our results reveal that inoculation success is predicable thereby enabling developments towards soil microbiome diagnostics as a tool for sustainable agriculture. mehr

Highly cited 2023

Highly Cited Researcher 2023

Klaus Schlaeppi: “Honored to be on Clarivate’s 2023 list of Highly Cited Researchers again. All thanks and credits to my GREAT team!”

MSc Sam

Congratulations Sam for your MSc degree!

In his MSc thesis ‘Growth Regulating Transcription Factors and Massilia bacteria in Plant Microbiome Feedbacks’, Sam investigated the involvement of Growth Regulating Transcription Factors in plant soil feedbacks by generating and testing grf mutants. Secondly, Sam isolated 316 bacteria strains from Arabidopsis roots and assembled with them a new strain collection. With both achievement, Sam established very useful group resources.

Study in PNAS: Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome

Diverse microbial communities colonize plant roots, where they feed on compounds secreted from their host plant. Lisa Thoenen has built a strain collection of maize root bacteria to study how they cope with benzoxazinoids, the main bioactive compounds secreted by maize. We find that bacteria strains differ greatly in their tolerance to benzoxazinoids and that tolerance against these selective antibiotic compounds depended on bacterial cell wall structure. We found that native root bacteria isolated from maize tolerated the benzoxazinoids better compared to nonhost Arabidopsis bacteria, suggesting adaptation of the root bacteria to specialized metabolites of their host plant. Importantly, we found that bacterial tolerance to the most abundant and most selective compound correlated significantly with the abundance of the bacteria on maize roots. This finding highlights bacterial tolerance to root-derived antimicrobial compounds as an underlying mechanism determining the community structure of host-specific microbiomes. mehr

fibl gruppenbild

Group outing at FIBL

On August 29th, we had a fantastic group outing to the FIBL in Frick. After an inspiring scientific exchange, we were given a very interesting tour of the institute. FIBL's hospitality was much appreciated and we enjoyed some amazing organic food. Later in the afternoon, we braved the rain with our colorful umbrellas and went for a hike on the famous "Chriesiwäg" and rounded off the day with a delicious ice cream. Thanks again to FIBL for hosting us! mehr


Study: Soil chemical and microbial gradients determine accumulation of root‐exuded secondary metabolites and plant–soil feedbacks in the field

4 August 2023
Valentin Gfeller and Selma Cadot performed a maize-wheat rotation experiment in a field with a strong soil gradient to study the context dependency of plant soil feedbacks. These feedbacks occur in response to plant release of exudates, which cause abiotic and biotic changes in the surrounding soil that then ‘feedback’ on the performance of the next generation of plants. Maize root exudates contain bioactive benzoxazinoids that can cause positive feedbacks on wheat yield. To test the effect of benzoxazinoids along the soil gradient, we grew wild-type and benzoxazinoid-deficient maize plants in the first year and then wheat in the second year. First, we confirmed the strong field gradient in soil chemistry and microbiomes. Because of the gradient, no feedback effects would be seen when simply averaging the data across the field. Instead we included the gradient into the calculations and detected pronounced feedbacks that gradually changed from negative to positive across the field. Yield was enhanced in one field corner, while being decreased in the other and this change of feedback can be explained by the standing chemical and microbial gradients. With this study we highlight that understanding within‐field soil heterogeneity is crucial for future exploitation of plant–soil feedbacks in sustainable precision agriculture. mehr


Study: Plant secondary metabolite-dependent plant-soil feedbacks can improve crop yield in the field

1 August 2023
In this work led by Valentin Gfeller, we studied the agronomic relevance of secondary metabolite mediated plant soil feedbacks. Plants secrete secondary metabolites from their roots to soil to alter the biotic and abiotic properties and this affects the performance of the next generation of plants. From greenhouse experiments we knew that maize-exuded benzoxazinoids impact the performance of wheat and here, we tested if these feedbacks occur in ‘real life’, i.e. in crop rotation in the field. We assessed three winter wheat varieties growing in field plots whose soils had been conditioned by either wild-type or benzoxazinoid-deficient maize plants. Following maize cultivation, we detected benzoxazinoid-dependent chemical and microbial changes in the soil, increase wheat biomass and also decreased insect herbivore abundance in benzoxazinoid-conditioned soils. Importantly, yield was increased by over 4% without a reduction in grain quality in benzoxazinoid-conditioned soils. Taken together, here we show that soil conditioning with plant secondary metabolites can increase yield via plant-soil feedbacks under agronomically realistic conditions. Hence, if these feedbacks function across different soils and environments, optimizing root exudation chemistry could be a powerful strategy to enhance crop yields without additional inputs. mehr


Study: A symbiotic footprint in the plant root microbiome

31 July 2023
In this study, conducted by Natacha Bodenhausen, Kyle Hartman and Marc Schmid, we explored how arbuscular mycorrhizal fungi (AMF) and rhizobium symbionts contribute plant root microbiome structure. We grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in natural soil and we characterized their root microbiomes. Besides plant phylogeny and species identity, we find that the type of symbioses also presented a significant driver of community composition. We find groups of microbes that were specific for the different symbioses and importantly, these ‘symbiosis footprints’ were also apparent removing the primary symbionts mycorrhiza and rhizobia from the dataset. Overall, we find evidence for microbiome imprints – which we term the symbiotypes – that reflect the symbiotic associations of the host plant. mehr


Study: Glyphosate and terbuthylazine effects on soil functions, microbiome composition and crop performance

13 July 2023
Veronica Caggìa led a study where we tested the hypothesis that herbicide application changes the soil microbiome that then negatively feeds back on plant growth. We found that bacteria were more sensitive to glyphosate and terbuthylazine application than fungi, but that herbicide application did not affect subsequent maize performance. We found that herbicide levels in soil varied a lot with time and soil moisture. This points to the importance of understanding the context-dependency of rapid herbicide degradation in order to avoid negative repercussions on non-target organisms and soil functions. mehr


Predicting soil fungal communities from chemical and physical properties

In this work led by Natacha Bodenhausen we developed code that allows to predict the composition of soil fungal communities based on physicochemical soil data using multivariate ordination. The idea behind is that reliable prediction of microbial communities from chemical soil properties, which farmers often have, could bypass the sequencing‐based generation of microbiota data, thereby making soil microbiome information available for agricultural purposes such as pathogen monitoring, field inoculation or yield projections. mehr


Congratulations Claudia for your MSc degree!

In her MSc thesis ‘Microbial community dynamics and their impact on plant performance under phosphorous limiting conditions’, Claudia studied the microbe-induced growth promotion of A. thaliana under P-limiting conditions. Examination of bacterial communities did revealed no major alteration of community composition in response to varying levels of P. However, she identified efficient phosphate solubilizing strains among the abundant root bacteria, which probably help the plants to mitigate stress by P-limitation. This work was motivated by the vision that phosphate solubilizing root bacteria can be used to enhance crop productivity in a sustainable way.


Picture «Maize root microbiome» was awarded in SNSF Scientific Image Competition

The picture submitted by Lisa Thönen shows extracts from maize roots on an agar plate containing plant specialized metabolites produced by maize, benzoxazinoids. The bacteria which can metabolise the compounds appear red. The jury commented: “The intriguing photograph acts as a poetic window into a new world awaiting discovery: the microbe communities living under our feet. We might not exactly know what we are looking at, but we still feel attracted to its material presence and enigmatic beauty. While the picture reminds us of both the micro- and macrocosmos, the container puts them on a human scale”. Each year the Swiss National Science Foundation awards images that researchers submit form their work. All pictures can be viewed here and covered by an article in SRF and NZZ. Pictures will be presented in the exhibition “Beauties of science” at the Biel Festival of Photography 2023 (5 – 28 May 2023).



Welcome Hilal

Hilal Civelek obtained her MSc degree from the Gebze Technical University in Turkey. Given her outstanding performance, Hilal has been awarded a PhD scholarship by the Turkish Ministry of Education. With her expertise in genetics, she will be working on the topic of the SNF project ‘Plant Responsiveness to Microbiota Feedbacks’.


Group retreat

Earlier in March, our recently grown group made their way to Engelberg for our first ever retreat. During our 3-day stay in the Zschokke-House on Gerschnialp, extensive science sessions were held, where we learnt more about what each group member is working on. Besides having exciting discussions and transfering knowledge, time was spent curling, skiing, snow tubing and hiking. Everyone is hoping for a next retreat to happen! mehr


Merci Jürg!

Thank you, Dr. Oetiker, for all your contributions to botany and teaching at the Basel University. What a memorable fare well party. We had lots of fun with your miracle fruits.


Welcome Mikiko

Mikiko Karasawa obtained a European Master degree in ‘Plant Health in Sustainable Cropping Systems’ after research stays in Valencia and Utrecht. In her PhD, she will investigate the underlying mechanisms of host specificity of plant microbiomes, specifically looking into the metabolic specialization of root microbiomes. Mikiko will work in the ERC project ‘Decoding microbiota feedbacks on plants – mifeePs’.


Welcome Anlun

Anlun Wei graduated with a Master’s degree at the Karlsruhe Institute of Technology. He will develop in his PhD methodology for the generation of bacterial mutant libraries. He will then apply this resource to uncover the genetics of maize root bacteria and their traits to cope with the secondary metabolites of their host plant. Anlun will work in the ERC project ‘Decoding microbiota feedbacks on plants – mifeePs’.


Welcome Ellen

Ellen recently completed her apprenticeship as laboratory technician. She has a background in agrobiology with special trainings in molecular biology and phytopathology. Ellen joins the team to become our robotics specialist for next generation sequencing applications and thereby, she holds a key position in the plant microbe interaction group


Welcome Christine

Christine obtained her PhD from the ETH Zurich where she continued as postdoc and senior assistant in the group of Prof. Julia Vorholt. She did seminal contributions to the field of phyllosphere biology, e.g. mapping metabolic interactions within the phyllosphere microbiome or demonstrating direct plant protection by the phyllosphere bacteria. Christine is a microbiologist with profound expertise in microbial genetics and bioinformatics. Christine will head the team working on the ERC project ‘Decoding microbiota feedbacks on plants -mifeePs’



Veronica Caggìa, Lisa Thoenen and Valentin Gfeller have successfully defended their PhDs. #PhDsisters #PhDbrother #dreamteam


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!
More pictures


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.
More pictures...


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!
More pictures


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’.