Opening the black box of microbial interactions: Microbiome editing on seed natural microbial communities

Over 80% of human food relies on plants, but up to 40% of crops are lost to pests and diseases. Chemical pesticides have boosted yields but pose health and environmental risks. To address this, the EU aims to replace 50% of pesticides with biological solutions by 2030.

As a result of hundreds of millions years of coevolution, plants host a diverse microbiota coming from soil, offering biotechnological potential. Exploring plant-microbe and microbe-microbe interactions can revolutionize agriculture, enhancing food security.

The discovered plant-beneficial microbial interactions could be used to generate tailored microbial communities, capable of protecting plants and reducing the need for pesticides.

CRISPR-Cas derived genetic tools to edit the plant seed microbiome in order to decipher the main microbial interactions affecting plant health.

SEEDITING aims to adapt these tools, analogous to reverse genetics, from simplified synthetic bacterial communities to native seed microbiota.

The main outcomes of the SEEDITING project will be to master an efficient tool for microbiome editing on SynComs (WP1) and to deploy this editing tool on extracted seed natural microbiota (WP2) to observe the consequences of editing on microbiome dynamics and microbial interactions in vitro.

Finally, I will assess the impact of seed microbiota editing on the microbial transmission rates to the seedlings and the resulting plant phenotypes (WP3).

This project will lead to major breakthroughs in microbiome sciences and plant-microorganisms interactions in agriculture by generating three main outputs opening new research avenues: 1) Validation of a microbiome editing tool transferrable to multiple ecosystems to decipher microbial interactions in natural communities. 2) Identification of microorganisms responsible for the modulation of host phenotypes. 3) Identification of microbial functions responsible for the phenotypes or involved in host colonization and survival.