One of the current challenge in agriculture is to achieve food security while mitigating adverse
environmental effects in a sustainable way. Chemical inputs and mechanization applied in
conventional agriculture significantly increased crop productivity by supporting food production
requests. On the other hand, the negative impact caused by the use of chemical inputs on the
environment (e.g. loss of biodiversity, soil degradation, etc.) and human health calls for the need to
develop more sustainable and productive faming systems less dependent to the use of pesticides
and limiting the losses related to pests. Promising findings highlighted that the untapped soil
microbiota diversity can influence plant tolerance and resistance to several pests. In light of this, a
challenge perspective in the modern agriculture is to design a new generation of green solutions
enable to increase plant resistance to biotic stresses for a more sustainable crop production.
However, the designing of specific plant synthetic microbiota needs for a better understanding of
the mechanisms underlying the plant microbiota interaction under a realistic ecological context. In
this context, based on a multidisciplinary consortium, and novel approaches DEEP IMPACT aims
at combining ecology, biology, plant genetics and mathematics to identify, characterize and validate
the microbial communities, plant communities and abiotic factors (including agricultural
managements) explaining variation in Brassica napus and Triticum aestivum resistance to several
pests. For this, we will start from an in situ approach by characterizing 100 fields (50 for each crop
species) for both habitat (climatic and edaphic variables) and biotic (microbiota, virome, weed
communities, pest attacks and pathobiota prevalence) features. Information from this broad
characterization, will be integrated in sparse and correlative statistical models to describe the
relative part of the variance explained by both habitat and biotic features and correlated with a
reduction of pest’s attacks. This analysis will allow to identify a combination of microbial species/and
soils correlated with an increase of crop’s resistance to pests. These microbial consortia will be
isolated by taking advantages of newly developed culturomics methods and characterized by both
whole genome sequencing and biochemical assays. Synthetic Consortia (SynComs) will be
reconstructed to test their efficacy on a broad range of pests attacking both crops. SynComs
carrying, beneficial, deleterious and neutral effects on plant resistance to pests will be tested in a
GWA study on a large panel of B. napus and T. aestivum genotypes to identify plant genetic loci
associated to SynComs responses and modulating disease caused by soil fungal pathogens
(Rhizoctonia solani – for oilseed rape – and Fusarium graminearum – for wheat). A novel, joint
GWA approach will be also developed in DEEP IMPACT to identify the interacting microbial/plant
genetic loci shaping the host-microbe interaction and associated with disease reduction. A
functional approach, based on metatranscriptomics and miRNA characterization, will be also
adopted to identify the functional modules in all the partners of the interaction (microbiota-plant-
pests) and to test the impact of microbiota diversity on plant miRNA secretion. DEEP IMPACT will
also investigate on the possible role of auxiliary plant species in modulating crop’s pest resistance
by indirectly act on the soil microbiota. A coming-back to the field scale will allow to test whether
the microbial association in conjunction with auxiliary plants are effective to protect crops against
natural pest’s infections/attacks under a broad range of pedo-climatic French zones. Overall, DEEP
IMPACT will contribute to the development of sustainable agricultural practices based on plant
microbiota to reduce current pesticides applications in agricultural settings.