Exploring functional and taxonomic rhizosphere microbiome signatures in drought-tolerant common beans

Abstract

Climate change-driven increases in temperature and water scarcity pose major threats to agricultural productivity. The rhizosphere microbiome plays a central role in plant responses to abiotic stress and represents a promising target for improving crop resilience. Here, we investigated the rhizosphere microbiomes of four common bean ( Phaseolus vulgaris L.) cultivars with contrasting drought tolerance under controlled water limitation. Using deep shotgun metagenomics, we constructed a rhizosphere gene catalog and recovered high-quality metagenome-assembled genomes to resolve taxonomic and functional profiles of the microbiome. Drought-tolerant genotypes were consistently associated with distinct quantitative microbial signatures, particularly enrichment of Actinomycetia and related functional pathways involved in osmoprotectant biosynthesis (e.g., trehalose, glycine betaine, and proline), oxidative stress mitigation, signal transduction, and nutrient cycling. Across genotypes, most genes and genomes were shared, indicating a stable core microbiome, while drought-tolerant cultivars showed a broader enrichment of stress-related taxa and functional traits within this shared background. These patterns suggest that drought primarily reshapes existing microbial functions rather than driving wholesale community replacement. Overall, our findings reveal genotype-dependent microbiome signatures associated with drought responses in common bean and provide a genome-resolved framework for identifying candidate taxa and functions for future validation. This study highlights the potential of microbiome-informed strategies to support crop resilience under water-limited conditions.