Plant-based growth media for discovering novel biocontrol rhizobacteria against soilborne fungal pathogens

Overview

Soil microbiomes contain a vast, largely untapped diversity of bacteria that produce secondary metabolites capable of suppressing plant pathogens. Conventional laboratory media fail to grow most of these organisms, limiting the discovery of new antimicrobial compounds. This solution introduces a plant-based growth media (PBM) pipeline that efficiently cultivates novel rhizobacteria from soil and root environments. Isolated strains are screened for biosynthetic gene clusters (BGCs) associated with secondary metabolite production, and the most promising candidates are assembled into consortia and tested in planta for biocontrol efficacy against soilborne fungal pathogens.

The approach addresses a critical bottleneck in agricultural biocontrol: access to previously uncultivable bacteria with novel antimicrobial potential. By combining innovative cultivation with molecular screening and greenhouse validation, the technology enables the development of microbial cocktails that can protect crops such as wheat and cucumber from fungal disease.

Technical specifications

• Plant-based growth media (PBM): Uses diluted plant extracts (e.g., wheat and cucumber) as growth substrates, enabling isolation of bacteria that cannot be cultivated on standard media such as LB or nutrient agar.
• Extended incubation: Plates incubated for up to 28 days at 30°C to recover slow-growing and rare taxa.
• Strain dereplication: Unique isolates identified through Eric-PCR fingerprinting and 16S rRNA gene sequencing.
• Molecular screening: Targeted amplicon sequencing detects novel secondary metabolite-encoding biosynthetic gene clusters (BGCs) in isolated strains.
• In vitro antifungal assays: Isolates and consortia tested against selected phytopathogens for antagonistic activity.
• In planta validation: Greenhouse trials with pathogen-challenged cucumber plants to compare disease-suppressive versus disease-conductive rhizosphere microbiomes using amplicon and long-read sequencing.
• Consortium design: Optimal strain combinations assembled into biocontrol cocktails for plant protection applications.

Technology readiness level

The PBM isolation pipeline has been validated in initial experiments, where wheat rhizosphere extracts yielded higher genus-level bacterial diversity on PBM compared with LB and nutrient agar, and several isolates were found to harbor novel BGCs. The next stage of validation involves a 14-month greenhouse study using cucumber plants challenged with a pathogenic fungus. This study will screen rhizosphere microbiomes from disease-suppressed and disease-conductive plants, build a large isolate library from suppressive rhizospheres using cucumber-based PBM, and evaluate optimized consortia for in-planta biocontrol performance. The technology is at the laboratory-validated stage, advancing toward greenhouse-confirmed proof of concept for agricultural deployment.