PSEUDOMICS
Exploiting the genomes of diverse pseudomonas biocontrol strains for sustainable agriculture, to protect the environment and to Improve Human Health by Production of Healthy Food

The success of agriculture in the European Union in producing healthy food is highly dependent on the suppression of phytopathogens, which cause major crop losses and decrease the quality of food. Biocontrol forms an environment-friendly alternative for chemical pesticides, the use of which is being strongly restricted in the EU since they are often harmful for the environment and human health. Pseudomonas is the most frequently used biocontrol bacterium. To be able to understand biocontrol and to come to an efficient application, this project will analyse the genomes of four Pseudomonas strains with different biocontrol mechanisms using functional and comparative analyses.

Objectives
A genomic approach is proposed for four (European) soil-borne Pseudomonas strains, which have the ability to protect plants against soil-borne diseases, usually caused by fungi using diverse mechanisms for their biocontrol ability.
The major objectives of the project are:
1) to generate high resolution, physical and genetic maps of the genomes of four Pseudomonas biocontrol strains
2) to use functional genomics of putative biocontrol genes of these strains in order to a) isolate novel biocontrol genes on the chromosomes and b), to produce micro-arrays dedicated to monitor biocontrol activity
3) to perform comparative genomics of Pseudomonas biocontrol genes in relation to putative biocontrol islands and evolution
4) as proof of principle: to study the expression of selected (putative) biocontrol genes, using dedicated micro-arrays under a variety of conditions, including industrial ones where biocontrol is applied.

Progress to Date
The project provides a wealth of information on genes and sequence data from four different Pseudomonas biocontrol strains that are relevant for their biocontrol ability and functioning in the rhizosphere. These data will provide a better understanding on how biocontrol inocula function and provide a solid basis for the more efficient application of inocula. The whole genome sequence (6x coverage) of one of the strains will reveal regulatory mechanisms that are involved in biocontrol and how this strains reacts on his environment.
Initially it was the objective of the proposal to produces a dedicated microarray which would be produced with Pseudomonas DNA fragments of genes essential for biocontrol of tomato foot and root rot. In the last part of the project ("proof of principle") we will check which genes are expressed under realistic biocontrol conditions in a greenhouse.

Results

Classified in ARABLE CROPS, CROP PESTS AND DISEASES, HUMAN HEALTH AND WELLBEING

Scientist responsible for the project