General Monitoring of biocontrol fungi in potting soils


Many crop protection products (including fungicides) are no longer available and alternatives are sorely needed. One alternative approach is to incorporate biocontrol organisms into the substrate that can constrain root fungi or pests. When testing biocontrol products such as Trichoderma, producers want to ensure the preferred organism remains sufficiently active within specific crops. Techniques to monitor these biocontrol fungi over time, sometimes down to the level of the specific strain used, are therefore required. Monitoring these fungi in a complex environment such as potting soil or on roots requires strain-specific detection techniques.

ILVO has experience in monitoring Trichoderma biocontrol fungi in substrates through classical plating on semi-selective media, a service offered through the Diagnostic Centre for Plants.

“This is sufficient in many cases, but the specificity is limited to the genus level of the organism, such as Trichoderma. If the specific strain also needs monitoring, a molecular detection assay can also be developed.

Kurt Heungens, ILVO researcher
Trichoderma on pink medium
Root segments colonized by Trichoderma plated on a semi-selective medium

First, a genetic study is conducted, where strain-specific fragments in the DNA of the target organism are identified via high-throughput sequencing (GBS). Subsequently, a specific qPCR assay determines the quantity of these fragments in the sample. Based on this quantity, the number of spore equivalents of the target organism can be calculated. This strategy was successfully implemented in collaboration with Biobest for a specific Trichoderma strain. This strain can now be monitored more accurately in various crops. The scientific results were recently published.
The full paper can be read here:

Biobest is proud to have developed a molecular detection tool for monitoring the biocontrol strain Trichoderma asperellum T34 in substrate, soil and plants. We are pleased about the collaboration with ILVO's Plant & Soil Living Lab.

Soraya França, Biobest researcher

This is the first time that the GBS-based strategy for identifying DNA markers has been applied for the development of a strain-specific qPCR assay for a biocontrol organism.

ILVO combines its expertise in both classical and molecular detection technology to help find specific solutions for producers of biocontrol organisms.

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