Efficient discovery pipeline for bioactive specialised metabolites in plant-associated microbes

Overview

This solution offers a flexible, highly efficient discovery pipeline for isolating and characterising bioactive specialised metabolites from plant-associated microbiomes. The approach is based on the principle that plant disease creates strong selective pressure, enriching for microbes that produce bioactive molecules capable of suppressing invading pathogens. By screening microbial communities from infected plant tissues, the pipeline identifies promising biocontrol candidates and the specialised metabolites responsible for their activity, supporting the development of new agricultural biocontrol products.

The pipeline has already been validated through two major research projects: one assessing soil Pseudomonas spp. interactions with Streptomyces scabies in UK potato fields, and another conducted in partnership with Zespri Group Ltd. to isolate biocontrol agents against kiwifruit canker (Pseudomonas actinidiae) in New Zealand. Both projects successfully identified effective bioactive bacteria and metabolites against target pathogens, confirming the underlying hypothesis.

Technical specifications

Key features:

• Collection of hundreds of potential biocontrol microbes from infected plant tissues
• Phenotypic screening for pathogen biocontrol activity
• Whole-genome sequencing of promising isolates
• Biosynthetic gene cluster identification using publicly available and proprietary bioinformatic and statistical analyses
• Genetic confirmation of key biosynthetic gene clusters essential for biocontrol
• In vitro characterisation of secreted bioactive molecules
• Applicable across a wide range of plant diseases and pathosystems

The pipeline integrates microbiology, genomics, bioinformatics, and biochemistry to move from environmental sampling to characterised bioactive molecules in a streamlined workflow.

Technology readiness level

The pipeline has been validated through two completed research projects, each demonstrating successful identification of effective bioactive bacteria and specialised metabolites against target pathogens. These prior successes confirm the central hypothesis and demonstrate the pipeline's reproducibility across different plant disease systems. Based on previous project timelines, an initial year-long project is expected to yield several promising bioactive candidates ready for further development and validation.