The BackToRoots research programme consists of four interconnected and complementary projects that, collectively, are aimed at ingeniously mining natural microbiomes and their associated plant traits, and to translate gained knowledge to next-generation crops that in concerted action with their microbiomes are better able to maximize growth and protection with less input of fertilizers and pesticides. Click on a project for a detailed description.

Project 1, 'Going back to the roots' has as its main aim to decipher the structural and functional diversity as well as the temporal dynamics of microbial communities in the spermosphere and rhizosphere of crop species and their wild relatives grown in agricultural and/or native habitats. Next to other economically important crops studied in WP1.1, specific emphasis is given in WP1.2 to the seed microbiome of common bean (Phaseolus vulgaris). To that end, close collaboration has been initiated with the University of Antioquia (Medellin, Colombia), with the International Centre of Tropical Agriculture (CIAT, Palmira, Colombia), and with Embrapa (Jagariuna, Brasil) for their expertise in bean cultivation and phenology, their large and well documented collection of common bean accessions and their knowledge of agricultural and native habitats. In close collaboration between the academic partners, we will identify constituents in seed and root exudates that trigger the proliferation and activity of specific beneficial microbial genera (read more).

Project 2, 'Innovation by nature' follows a sophisticated, multidisciplinary approach with model and crop species i) to characterize early root cell-type specific molecular changes that are initiated by beneficial microbes and are crucial for stimulating plant immunity and/or plant growth (WP2.1), and ii) to identify microorganisms that are selectively enriched in the root microbiome when plants are under pathogen pressure and identify plant cues involved in this selection (WP2.2). In this workpackage, we will investigate the dynamics and functioning of the root microbiome of Arabidopsis and crop plants in response to infection by necrotrophic and biotrophic pathogens. We will test the ‘crying for help’ hypothesis, i.e. the selective stimulation of beneficial microbes by plants under stress, a task conducted in close collaboration with the academic groups in projects 3 & 4 (read more).  

Project 3, 'Microbial support of plant growth under abiotic stress' has a major emphasis on deciphering the role of the seed and root microbiomes on plant growth under abiotic stress. More specifically, we will identify the core microbiome from native plant species grown in desert habitats (WP3.1) and determine how these microbial consortia contribute to abiotic stress tolerance of plants. To be able to conduct quantitative studies, an assay will be developed to monitor plant performance under abiotic stress conditions (drought, heat, salinity, nutrient limitations) in response to selected microorganisms (WP3.2). Plant growth, leaf surface, photosynthetic performance, and seed production will be assessed using non-destructive digital phenotyping. Based on these results, key strains identified in the seed and root microbiomes (projects 1 and 3) will be identified and used for reconstructing microbiome populations that in turn will be tested for their influence on abiotic stress tolerance (WP3.3) (read more).

Project 4, 'Plant protection on demand' focuses specifically on symbiotic actinomycetes, a reference panel of 20 isolates from native habitats and isolates obtained in projects 1 and 3, and will determine how plants activate antimicrobial production in these actinomycetes for their own benefit. Special attention will be given in WP4.1 to the role and identity of plant hormones and constituents in root and seed exudates that activate the production of yet unknown antimicrobial compounds by actinomycetes. To go beyond the one-microbe-at-a-time approach, WP4.2 will focus on competition-mediated activation of novel antimicrobials in an existing test panel and new collections of actinomycetes. WP4.3 will elucidate the nature of the antimicrobials and identify the most promising lead compounds for further valorization (read more).