Metagenomic bioprospecting of kei apple rhizosphere microbiome for plant growth-promoting genes and metabolites

Overview

This project applies metagenomic bioprospecting to the rhizosphere of kei apple trees to unlock the metabolic potential of unculturable soil microbes. More than 99% of environmental microorganisms cannot be grown in the laboratory using standard culture techniques, leaving a vast reservoir of potentially valuable genes and metabolites unexplored. By using cultivation-independent methods, the project aims to discover new plant growth-promoting (PGP) genes and bioactive metabolites that can support sustainable agriculture and reduce dependence on synthetic fertilizers.

The work builds on prior laboratory experience demonstrating that rhizobial strains and mycorrhizal fungi can alleviate drought stress and improve the yield, seed size, and fat content of soybean. The kei apple rhizosphere represents an underexplored ecological niche that may harbor novel microbial functions with direct applications in crop productivity and stress tolerance.

Technical specifications

Research approach:

• Replicate rhizosphere soil samples collected from kei apple trees across multiple geographic locations
• Direct extraction and purification of genomic DNA from rhizosphere soil, bypassing culture-dependent isolation
• Shotgun metagenomic sequencing to capture the full genetic content of the microbial community
• Bioinformatic assembly of metagenome-assembled genomes (MAGs) to reconstruct individual microbial genomes
• Screening of MAGs for novel PGP genes and metabolic pathways, including nitrogen fixation and stress tolerance functions
• Cloning and application of promising gene cassettes for evaluation as plant growth-promoting inoculants

Relevant prior findings:

• Rhizobium sp. isolates carrying the coniferyl aldehyde dehydrogenase gene associated with nitrogen fixation
• R. cellulosilyticum strain R3 carrying cysteine activity genes linked to nitrogen fixation
• Microbial inoculants shown to enhance growth, increase mycorrhizal spore counts, and raise root colonization rates under drought conditions of 100%, 70%, and 40% field capacity

Technology readiness level

The project is at an early-to-mid research stage. Foundational laboratory work has validated the ability of rhizobial and mycorrhizal inoculants to improve drought-stressed soybean performance in greenhouse pot experiments using a completely randomized design with 24 treatments and 8 replicates. The next phase extends this work into metagenomic exploration of the kei apple rhizosphere, transitioning from culture-dependent validation to culture-independent gene discovery. Identified MAGs and candidate PGP genes will require further cloning, functional validation, and field-level testing before commercial deployment in agricultural biotechnology applications.