The overarching aim of AGRIBIOME is to further advance sustainable crop production by exploiting microbiome-mediated disease resistance. 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.
One of the major challenges faced by 21st century agriculture is to achieve food security under changing climatic conditions while mitigating adverse environmental effects in a sustainable way. Plant-associated microbiomes have a tremendous and so far untapped potential to improve plant resilience to abiotic and biotic stresses and, ultimately, crop yield. The ongoing discoveries of novel plant microbiome functions resulted in a boost of research efforts aimed at capitalising on plant-associated microbial communities for sustainable crop production. These discoveries are effectively paving the way for the second Green Revolution and Swiss researchers are at the forefront of these innovations. However, the scientific enthusiasm has led to a fragmentation of the research landscape: valuable discoveries based on plant-microbiota interactions often lack the agro-ecological context needed to accelerate translation into innovative applications for sustainable agriculture. AGRIBIOME will fill these knowledge gaps by drawing upon the combined expertise of researchers, breeders, farmers, and extension services to develop a unique multi-disciplinary experimental framework. In particular, different approaches will be integrated in this project to characterise the impact of plant genetics and microbial inoculants to engineer a functional plant microbiome resulting in enhanced crop performance. Akin to the role of the gut microbiome in human health, root biodiversity can be considered as a reservoir of “plant probiotic” microorganisms deployable to enhance sustainable crop yield.
AGRIBIOME will use targeted plant-microbe interactions to tackle one of the most severe problems in global protein production. Soil-borne diseases in legumes, especially in pea (Pisum sativum L.), cause severe damage and can lead up to total yield loss. The lack of adequate resistance in current pea varieties against a complex of different soil-borne diseases impedes pea cultivation worldwide. The overall goal is to improve the resistance of pea against soil-borne diseases to allow higher frequencies of grain legumes in farming systems.
The main innovations of AGRIBIOME include (i) novel crop selection concepts based on holobiont genetic markers (ii) application of resistance-related microbiome data to crop plants addressing major limitations of legumes and sustainable protein production that could not yet been solved by uni-disciplinary approaches (iii) design of new microbial applications that manipulate the functional root microbiome in a predictable manner, (iv) implementation of project outcomes in the breeding programme of a commercial breeding company and (v) the opportunity to transfer project outcomes to breeding programmes of other crop species and cultivation issues (incl. other biotic and abiotic stresses).