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.
In the first year of the project sequencing pre-tests were performed with our sequencing service in order to optimise our approach to characterise the bacterial and fungal microbiome of diseased pea roots. Finally, over 1200 root samples of 312 pea genotypes that grew in a replicated greenhouse resistance experiment on pathogen infested field soil could be processed and sent for sequencing. Moreover, we have run several pre-tests for the SNP-genotyping of the 312 pea genotypes. These samples are currently being sequenced. The finalised data analyses of the microbiome and pea SNP sequencing data sets (MS1.1 and MS1.2) are expected for 2021 (Q2-Q4).
A pot experiment was conducted to characterise the pea root rot complexes via quantitative real-time PCR. The resulting manuscript has now been submitted to the journal Plant, Cell & Environment entitled “Untangling the pea root rot complex reveals microbial markers for plant health”.
Persons involved in the project
Dr. Pierre Hohmann
, project leader, Senior Scientist, FiBLDr. Monika Messmer
, Head of Plant Breeding, FiBL, Prof. Dr. Bruno Studer
, Head of Molecular Plant Breeding, ETH ZurichLukas Wille
, PostDoc, Plant Breeding Group, FiBLDr. Martin Hartmann
, Senior Scientist, Sustainable Agroecosystems, ETH ZurichDr. Klaus Oldach
, Pre-breeder, KWS Saat SEDr. Nora Temme
, Manager Biologicals, KWS Saat SEHerbert Völkle
, Director of Swiss organic breeder Getreidezüchtung Peter Kunz
Last update to this project presentation 18.05.2021