Isolation of Novel Anti-Phytopathogen Agents from Soil Bacteria Using Metagenomic Tools

Isolation of Novel Anti-Phytopathogen Agents from Soil Bacteria Using Metagenomic Tools

Funding Body (EPA, FP7, etc): Department of Agriculture, Fisher and Food

Project type (PhD, post-doc, etc): post-doc

Period (start to end): Aug 2008 – July 2011

Researcher: Ruth Henneberger

Project Description 

The demand for novel agents for the control of plant diseases has increased significantly in recent years due to legislation to reduce the application of toxic chemicals and the emergence of pathogens resistant to currently available products. The microbiota of soil is known to be a rich source of such novel antimicrobial and antifungal substances. Although soil represents one of the most diverse ecosystems on earth, the majority of microorganisms have yet to be cultured, and only a small fraction of the soil microbial diversity can currently be exploited using culture-dependent techniques. In this study, a culture-independent metagenomic based approach is being applied to analyse prokaryotic soil communities for the presence of novel anti-pathogen agents against phytopathogenic bacteria and fungi of relevance to Irish agriculture. Agricultural soil samples from organic field trials that showed natural suppression of plant diseases were selected for this study. Fosmid metagenomic libraries, which contain environmental genomic DNA inserts (approx. 40 kb in size) extracted from the total microbial communities of these samples, are screened for the presence of metagenomic clones with anti-microbial activity against certain plant pathogens. Clones with anti-pathogen activity will be further analysed to determine the DNA sequences and origins of the genes involved, and to characterise the active compounds produced. In a complementary culture-dependent approach, microbial genera that have been isolated from the agricultural soil samples are screened for their anti-pathogen activity.

Environmental Research Institute

University College Cork, Lee Road, Cork