Heritable microbiome variation is correlated with source environment in locally adapted maize varieties

Area of Science:

• Plant-microbe interactions
• Genomics
• Agricultural science

Background:

• Beneficial plant-microorganism interactions are crucial for crop health and resilience.
• The heritability of plant microbiomes and host genetic control over these interactions under stress remain poorly understood.

Purpose of the Study:

• To investigate the influence of host plant genotype and environment on root and rhizosphere microbiome composition in locally adapted maize.
• To identify host genetic mechanisms modulating plant-microbiota interactions under stress conditions.

Main Methods:

• Surveyed 3,168 root and rhizosphere microbiome samples from 129 Zea accessions across diverse habitats and conditions.
• Quantified effects of stress treatments and host genotype on microbiome composition.
• Performed genome-wide association analysis to identify host genetic variants linked to microbiome abundance and environmental factors.

Main Results:

• Plant genotype and source environment significantly predicted microbiome abundance.
• Identified host genetic variants associated with rhizosphere microbiome composition and environmental adaptation.
• Discovered transposon insertions in a gene linked to the bacterium Massilia and soil nitrogen levels.

Conclusions:

• Locally adapted maize varieties exhibit genetic control over their root and rhizosphere microbiomes, reflecting adaptation to their native environments.
• The bacterium Massilia, when isolated and inoculated, enhances root development, biomass, and adaptation to low nitrogen conditions.
• Host genetic mechanisms play a role in modulating plant-microbiota interactions for stress tolerance in maize.