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Deciphering of Root and Rhizosphere microbiome to increase host fitness in the Fusarium oxysporum - plant interaction . (DIRECTION)

Fungi have a devastating impact on human nutrition and health. Fungal pathogens provoke huge yield losses in crops, destroying around 23% of the agricultural production annually. A major proportion of this loss is caused by pathogenic root-colonizing microbes that have evolved sophisticated strategies to outcompete the benign microbial competitors in the rhizosphere and to actively suppress the plant immune response. The fungal pathogen Fusarium oxysporum (Fox) is a soil-borne root infecting fungus that provokes vascular wilt disease in over a hundred different agricultural crops, and represents a serious threat world-wide. The current control methods for this pathogen depend upon extensive use of chemical pesticides, which are highly unsustainable in the food-chain. Here we propose to use the Fox-tomato interaction as a model to molecularly dissect the role of the root (including endophytic) and rhizosphere microbiota in modulating vascular wilt disease.
We will use a barcoded pyrosequencing approach to taxonomically define the root and rhizosphere microbiome in tomato. Next, we will dissect the impact of the microbiome on fungal host sensing, using an established collection of isogenic signalling mutants of Fox available in the host lab. We will carry out in vivo Fox- bacterial interaction assays to generate a dataset for identification of bacterial communities exerting an antagonistic effect on pathogen colonization. The project will thus produce new insights into the interplay between the root microbiome and pathogen colonization. The, generated knowledge platform will be used to reassemble a synthetic ‘SynCom' microbiome that will be used to control Vascular Wilt, thereby advancing the development of sustainable agriculture.

Universidad de Córdoba

Objective 1: Define the culturable microbiome from healthy and infected tomato plants upon interaction with F. oxysporum f. sp. lycopersici and define tomato-specific microbial differentials.
Objective 2: To understand the effect of major identified bacterial root and rhizosphere phyla on F. oxysporum-tomato interaction in vitro and in vivo by using an isogenic Fox mutant collection from host lab.
Objective 3: Generate a complete Core synthetic microbiome community to resist Fox in tomato and determine its modulation by standard soil parameters such as pH and fertilizer application.

- D1.1 Publication 1. Fusarium oxysporum alters host microbiome during colonization of tomato (Obj 1 and 2).
- D2.1 Publication 2. Generation of a Synthetic microbiome as an efficient means of biological control against Fox (Obj 3).
- D3.1 Publication 3. Opinion article on Synthetic microbiome in sustainable agriculture to control pesticides and diseases (Obj 3).

The Project enhance the future career prospects of the researcher after the fellowship in these impacts:

- to improve of professional profile by increase of scientific skills;

- to establish a collaboration network beyond the host institution and provide international visibility and strength of network capacity;

- to increase of European R&I visibility;

- to generate an impact on European society including the science base and/or the economy, it based on the work in diferents research centers (Indian Research System, University of Bremen in Germany, University of Cordoba in Spain) and the collaboration with a different research groups from consortium "Introducing non-flooded crops in rice dominated landscapes: Impact on CarbOn, Nitrogen and water budgets (ICON)"


Genética Molecular de la Patogénesis Fúngica

Code PAIDI: BIO-138

Antonio C. Di Pietro . Coordinator. 

Universidad de Córdoba

Budget of Andalusian group: € 170,121.60

Keywords: Microbial Ecology, Fusarium, Tomato, synthetic biology, Microbiome
Duration: 24 months. September, 1th 2018 to August, 31th 2020
Project cost: € 170,121.60