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Every project supported by Gebert Rüf Stiftung is made accessible with a web presentation that informs about the core data of the project. With this public presentation, the foundation publishes the funding results achieved and contributes to the communication of science to society.


AGRIBIOME – Plant Microbiome Recruitment for Superior Agricultural Systems


The project management is responsible for the content of the information provided.

Project data

  • Project no: GRS-082/19 
  • Amount of funding: CHF 299'000 
  • Approved: 30.10.2019 
  • Duration: 04.2020 - 03.2024 
  • Area of activity:  Microbials, seit 2016

Project management

Project description

AGRIBIOME will advance sustainable crop production by developing novel, microbiome-based breeding tools. These tools will generate resilient plants recruiting a functional microbial community that synergistically interacts with its host.
We envisage that microbiome-based ecosystem services can be steered by bio-inoculation and breeding. The main goals of AGRIBIOME are to (i) identify microbial hubs (highly connected taxa in microbial networks) regulated by plant genotype while mitigating biotic stresses, (ii) develop molecular markers for plant traits associated with recruitment of beneficial microbes, (iii) establish a new generation of plant probiotics that predictably and consistently enhance crop resilience and (iv) utilise knowledge on microbiome engineering to predict crop disease resistance towards holobiont-based breeding programmes. The outcome of this project will set a precedent for other crop species and cultivation issues employing the holobiont concept that regards the crop species as an ecological unit consisting of the plant and its associated microbial community.
AGRIBIOME will develop innovative tools to harness microbiome functions for breeding and seed health strategies while addressing the demand for less dependency on soybean imports and fuel-based inputs, thus, achieving more sustainable and circular food production in Europe as requested by civil societies and policy makers. This will strengthen environmental and climate-smart primary plant production and provide consumers with healthy and safe food along with affordable diets.


AGRIBIOME has finalized the GBS genotyping of the panel of 254 pea lines which had been phenotyped for their resistance towards soil born root rot in infected field soil under controlled conditions. GWAS revealed one major QTL for root rot resistance on Chromosome 6 explaining up to 16% and encompasses a gene for an EF hand associated protein. Genomic prediction models can explain up to 50% of the variation for the observed root rot resistance. Scientific publication is in process. We have conducted amplicon sequencing to determine the microbial community (PacBio for ITS region for fungi; MiSeq of 16S rRNA for bacteria) of pea roots grown in infected soil for the whole panel of 254 pea lines with at least 4 biological replications. The pea genotype had a significant effect on the fungal and bacterial diversity indices, while the origin of the pea lines (genetic resources; European cultivars; Swiss breeding lines) was of minor importance. Key fungal and bacterial OTUs linked to root rot resistance have been identified based on bulk segregant analysis and network analysis is ongoing. GWAS will be conducted for selected OTUs to identify host plant genomic regions responsible for the selective recruitment of microbiome taxa. In a next step GWAS for root rot resistance will be conducted following a holobiont approach by combining plant genotypic SNP data and OTU frequencies. This will allow to disentangle direct plant resistance from microbiome-mediated plant resistance. Most significant SNPs will be converted into KASP marker in order to conduct marker assisted selection of pea breeding material for direct and microbiome-mediated disease resistance. Validation of the different selection schemes will be done in field trails. Most contrasting pea lines based on phenotypic data have been tested in replicated field trials in 2021 and 2022 on a Swiss field with severe symptoms of soil fatique. 15 pea plants per plot have been uprooted during flowering time, assessed by root rot disease score index and sampled for root microbiome analysis. Analysis of data is ongoing. These lines were also multiplied in 2022 to be available for further research. AGRIBIOME is a multidisciplinary and multi-actor team of FiBL with close collaboration with large scale breeding company KWS AG, small organic breeder Getreidezüchtung Peter Kunz and experts of the ETH Zurich: Prof Bruno Studer for molecular plant breeding, and Prof. Martin Hartmann microbiome analysis. AGRIBIOME is co-founded by European projects in order to fully exploit the unique dataset and pathing the way for breeding resilient cultivars through recruitment of beneficial microbiome community and for developing microbial seed inoculants as alternative to synthetic seed treatments.


Persons involved in the project

Valentin Gfeller, Project lead, Scientist Microbiome-assisted breeding, FiBL
Dr. Monika Messmer, Head of Plant Breeding, interims project lead, FiBL
Natacha Bodenhausen, Team Leader microbiome, FiBL
Michael Schneider, Scientist for MAS and genomic prediction, FiBL
Prof. Dr. Bruno Studer, Head of Molecular Plant Breeding, ETH Zurich
Daniel Ariza Suarez, PhD Molecular Plant Breeding, ETH Zurich
Dr. Martin Hartmann, Senior Scientist, Sustainable Agroecosystems, ETH Zurich
Dr. Klaus Oldach, Pre-breeder, KWS Saat SE
Dr. Nora Temme, Manager Biologicals, KWS Saat SE
Herbert Völkle, Director of Swiss organic breeder Getreidezüchtung Peter Kunz

Last update to this project presentation  20.11.2023