Multi-omics platform for analyzing root microbiome defense against plant-parasitic nematode invasion

Overview

This research platform applies multi-omics approaches to uncover how root-associated microbiomes reassemble and function during plant-parasitic nematode invasion. While arbuscular mycorrhizal fungi and plant growth-promoting rhizobacteria are known to reduce root-knot nematode infection, the mechanisms by which the broader root microbiome reorganizes in response to nematode attack remain poorly understood. By integrating metagenomic, metatranscriptomic, and metabolomic analyses of cotton roots and rhizospheric soil, this work reveals the molecular and microbial dynamics that drive natural nematode resistance. The findings support the development of microbiome-based crop protection strategies that reduce dependence on chemical nematicides.

Technical specifications

Core capabilities:

• Time-course bioassay of cotton seedlings under controlled conditions comparing healthy soil, unhealthy soil, and autoclaved controls
• Metagenomic profiling of fungal and bacterial communities in roots and rhizospheric soil
• Metatranscriptomic analysis to capture functional gene expression of the root microbiome during nematode invasion
• Metabolomic profiling of root and soil samples to identify metabolites associated with nematode defense
• Sampling at weekly intervals following nematode inoculation to track microbiome reassembly dynamics
• Field-validated baseline data from over 30 identified plant-parasitic nematode species affecting cotton health and yield

Key research insights:

• Crop rotation farmland with higher microbial richness and soil nutrition correlates with greater cotton resistance to nematode invasion
• Integration of multiple omics layers enables a systems-level understanding of microbiome-mediated plant defense

Technology readiness level

The research is grounded in completed field investigations at the University of Florida's NFREC, where nematode diversity and impacts on cotton have been characterized. The next phase involves controlled laboratory bioassays to validate microbiome reassembly mechanisms. This work is at an early-to-mid stage of scientific validation, transitioning from observational field studies to mechanistic laboratory investigation with multi-omics characterization.