Farming system shapes rhizosphere microbiota and root gene expression in common bean

The rhizosphere is a dynamic interface where plant roots and microorganisms interact through the exchange of metabolites and signaling molecules. This study evaluated the impact of organic and conventional farming on the rhizosphere microbiota and root gene expression in common bean by integrating metabarcoding (16S rRNA and ITS) and RNA sequencing (RNA-seq) approaches. Bacterial alpha diversity was higher in the rhizosphere of plants grown under conventional than under the organic system (2961 vs. 1532 Amplicon Sequence Variants (ASVs) observed), whereas fungal alpha diversity was greater in the organic system (372 vs. 321 ASVs observed). The fungi-to-prokaryote ratio was approximately twofold higher in organic systems. Organic farming promoted Funneliformis , Metarhizium , Chitinophaga , and Rhizobium , while conventional farming favored Pirellula , Terrimonas , and Mortierella . Transcriptomic analysis identified 5511 differentially expressed genes (DEGs), of which 1085 showed |log 2 FC| ≥ 2, mainly upregulated under organic conditions. These genes were enriched in functions related to secondary metabolism, redox homeostasis, hormone signaling, nodulation, and nutrient transport. DEGs involved in the synthesis of root exudate metabolites, including fatty acids, indolic compounds, and organic acids, were also identified, highlighting their potential role in microbial recruitment. Downregulated genes were associated with cell cycle and kinase activity. Correlation analyses linked beneficial fungal taxa with the induction of genes related to plant growth, defense, and symbiosis. This work provides a basis for future studies aimed at identifying key genes involved in root development and plant–microbe interactions, potentially improving breeding programs for cultivar resilience and efficiency.