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) utilize 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 started in 2020 by genotyping a panel of 254 pea lines. These pea lines had previously been phenotyped for their resistance towards root rot when grown in infested field soil under controlled conditions. Genome-wide association studies (GWAS) revealed one major genomic region on chromosome 6, explaining up to 15% of the observed root rot resistance. Further analysis revealed that genomic prediction models can explain up to 50% of the observed variation in root rot resistance. To understand the relationship between root rot resistance and the root microbiome, root fungal and bacterial communities were determined by amplicon sequencing of the whole panel of 254 pea lines grown under root rot stress. The pea genotype showed substantial effects 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. Microbiota community composition was associated with the resistance level of the pea against root rot. Key fungi and bacteria linked to root rot resistance have been identified. Some of these potentially beneficial microbes were shown to be highly heritable and highly connected within the microbial network (hub taxa). GWAS were conducted to find plant genomic regions associated with microbiome features and individual microbes related to disease resistance. Several genomic regions were found to affect the abundance of potentially beneficial microbes. The strongest correlation was found at the same genomic locus on chromosome 6 as for the disease resistance. Next, GWAS on root rot resistance were conducted following a holobiont approach by incorporating plant genotypic data and the abundance of individual microbes. The holobiont approach markedly increased the prediction ability of pea root rot resistance.
Based on our findings, plant genetic markers were developed for root rot resistance and the recruitment of potentially beneficial microbes. These markers were used to screen the breeding lines of two breeding companies. In future collaborations, these markers will further be applied to conduct marker-assisted selection for direct and microbiome-mediated disease resistance. Validation of the different selection schemes will be done in field trials. Within this project, the disease resistance of the most contrasting genotypes was validated in replicated field trials in 2021, 2022 and 2023 on a Swiss field with severe symptoms of soil fatigue triggered by root rot pathogens. In parallel, the first bio-inoculation experiments with potentially beneficial microbes have been conducted at three research sites in Switzerland and Germany.
AGRIBIOME is a multidisciplinary and multi-actor team led by FiBL in close collaboration with the large breeding company KWS AG, the non-profit organic breeder gzpk and experts from ETH Zurich: Prof. Bruno Studer for molecular plant breeding and Dr. Martin Hartmann for microbiome analysis. AGRIBIOME delivered promising results for future research on breeding resilient cultivars through the recruitment of beneficial microbial communities and developing microbial seed inoculants as an alternative to synthetic seed treatments.
AGRIBIOME acted as a catalyst, sparking several research projects and collaborations on the same topic. This has resulted in various follow-up projects. To further explore the implementation into practice, a field experiment was financed by the Association of the Swiss Organic Agriculture Organizations (Bio Suisse). The markers established in AGRIBIOME are being further tested and used in the Horizon Europe Root2Res project together with KWS. Further, collaborations within the AGRIBOIME project facilitated the establishment and implementation of the Swiss Plant Breeding Center (SPBC) as a service provider for public and private breeders in Switzerland, supported by the Federal Office for Agriculture. As a hub of breeding innovations, the SPBC will also cover the topic of microbiomes in breeding in its portfolio. In an innovation project for plant breeding, the SPBC and FiBL assist the breeding company gzpk in an AGRIBIOME follow-up project on plant-microbe interactions. In the Horizon Europe LiveSeeding project, FiBL will also apply the expertise gained within AGRIBIOME to seed microbiomes.