BioMatNet Item: QLK3-2002-02068 - Soil meta-genomics to identify novel mechanisms of antagonism and antifungal activity for the improved control of phytopathogens (METACONTROL)

[BioMatNet Database - FP5 Quality of Life Programme]

QLK3-2002-02068
Soil meta-genomics to identify novel mechanisms of antagonism and antifungal activity for the improved control of phytopathogens (METACONTROL)

Contacts

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Type of Project	Shared Cost Research
Contract No	QLK3-2002-02068
Total Cost
EC Contribution	1,565,846 EUR
Start Date	01-10-2002
Duration	36 MONTHS

Abstract

This project will explore and exploit the anti-phytopathogen diversity present in selected European suppressive soils representing a wide geographical spread. The untapped functional potential present will be accessed using metagenomic cloning of soil DNA. Moreover, as a baseline, antagonistic organisms will be isolated. Libraries constructed on the basis of the total and active cell fractions, as well as the isolates, will be screened for anti-phytopathogen functions. Selected clones will be assayed with respect to the nature of the antagonistic compounds and production loci, involving sequencing. Potential producer strains will be modified so as to optimise gene expression, growth and stability. Based on the gene sequences obtained, molecular tools will be developed and validated for monitoring of soil suppressiveness. The potential of marketable applications will be assessed.

Objectives

The objectives of the project are:

optimise a robust strategy to obtain high-quality DNA from total and active micro-organisms in soil.
clone the metagenome from the total and active micro-organisms from four selected European suppressive soils.
obtain a suite of operons that produce novel anti-phytopathogenic compounds from the soils under study.
obtain a suite of anti-phytopathogen production loci from antagonists isolated from the soils under study.
understand and, if feasible, optimise the expression levels of selected anti-phytopathogen production loci as well as organisms, resulting in strategies for production.
produce and validate molecular tools for monitoring soil suppressiveness status.

Activities

The work under this project will focus on the exploration and exploitation of the anti-phytopathogen microbial diversity present in European phytopathogen-suppressive soils. A selection of four soils in four European countries will be analysed, ensuring a wide geographical spread and European dimension. As a baseline, a collection of isolates with anti-phytopathogen activity will also be obtained from these soils. Key to the project will be the application of an advanced molecular tool, metagenomic cloning of high-quality soil DNA, for the production of clone libraries. This represents a significant step forward in comparison with previous studies, as the untapped anti-phytopathogen potential present in the unculturable soil microbiota (often >95% of the total) will be accessed. Both the active and the total microbiota in the selected soils will be targeted. To obtain the active cell fractions, microbial cells from soil will be marked with metabolic stains, after which they will be sorted by flow cytometry. Following the production of metagenomic clone libraries, as well as libraries from the (baseline) antagonistic isolates, functional as well as genetic high-throughput screenings will be performed to provide a selection of clones with robust anti-phytopathogen activity. A preset number of such clones per library will be analysed with respect to the spectrum of action versus other target and non-target organisms, the minimal productive unit and its sequence, and the expression level as well as ways to optimise it. In parallel with the genetic approach, the anti-phytopathogen compounds produced will be identified using biochemical methods. Novel strains, production loci and compounds will be protected, to provide oppotunities for future production. On the basis of the sequence information, molecular tools will be developed and applied to monitor the specific suppressive status of soils.

Deliverables

The main deliverables to be obtained in the course of METACONTROL are:

suppressive soils characterised, HMW DNA produced, antagonists isolated.
soil metagenomic clone libraries completed.
clones with anti-phytopathogen activity selected.
anti-phytopathogen compounds (partially) identified.
minimal productive units defined and expression optimised.
production strains and strategies for production available, patents if applicable.
molecular tools for monitoring suppressive status of soils developed and validated.

Contacts

Coordinator

J.D. van ELSAS / Plant Research International Crop and Production Ecology / NETHERLANDS

Participant