Decoding microbial diversity in roots of rice plants under flooded conditions: influence of the host genotype, root compartment, and mycorrhizal association.

Flooded rice roots show compartment-specific microbiomes, with bacterial taxa comprising ~95% of total microbes, and rice genotype and AM status reshaping community composition.

• Why it matters: Limited knowledge exists on how flooded-condition root microbiomes differ by host genotype, root compartment, and arbuscular mycorrhizal association, despite AM fungi being able to colonize under flooding.
• What they did: Metagenomic sequencing profiled root endosphere and rhizosphere microbiomes in cultivated rice under flooded conditions, comparing host genotypes and plants pre-inoculated with Rhizophagus irregularis.
• The result: Root compartment and genotype significantly influenced microbiome composition, with most genotype-specific recruitment at the species level, and functional gene abundance showing compartmentalization of nutrient-cycling bacteria.

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